Mitochondrial DNA rates and biogeography in European newts (genus Euproctus)

Systematic Biology

Volumn 46, Issue 1, 1997, Pages 126-144

  Caccone, Adalgisa ^a,b   Milinkovitch, Michel C ^b   Sbordoni, Valerio ^a   Powell, Jeffrey R ^b  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b YALE UNIVERSITY   (United States)

Author keywords

Biogeography; Cytochrome b; Euproctus; Mitochondrial DNA rates; Mitochondrial ribosomal genes; Molecular clocks; Triturus

Indexed keywords

AMPHIUMA MEANS; CAUDATA; EUPROCTUS; EUPROCTUS MONTANUS; EUPROCTUS PLATYCEPHALUS; PLATYCEPHALUS; PLEURODELES WALTL; SALAMANDRIDAE; TRITURUS; TRITURUS CARNIFEX; TRITURUS VULGARIS; VERTEBRATA;

CYTOCHROME B; MITOCHONDRIAL DNA; RIBOSOME RNA; RNA 16S; RNA, RIBOSOMAL, 12S;

ANIMAL; ARTICLE; CLASSIFICATION; EUROPE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SALAMANDER; SEQUENCE HOMOLOGY; SOUTHERN EUROPE; TIME;

ANIMALS; BASE SEQUENCE; CYTOCHROME B GROUP; DNA, MITOCHONDRIAL; EUROPE; EVOLUTION, MOLECULAR; GEOGRAPHY; MEDITERRANEAN REGION; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; SALAMANDRIDAE; SEQUENCE HOMOLOGY, NUCLEIC ACID; TIME FACTORS; VARIATION (GENETICS);

EID: 0031084474     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1093/sysbio/46.1.126     Document Type: Article

References (107)

1. ACCORDI, F., E. GRASSI MILANO, AND V. P. GALLO. 1984. The adrenal gland of Euproctus (Urodela, Salamandridae): Comparison of the three species and phylogenetic inferences. J. Anat. 139:209-214.
2. 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.
3. ALLARD, M. W., M. M. MIYAMOTO, L. JARECKI, F. KRAUS, AND M. R. TENNANT. 1992. DNA systematics and evolution of the artiodactyl family Bovidae. Proc. Natl. Acad. Sci. USA 89:3972-3976.
4. ALVAREZ, W. 1972. Rotation of the Corsica-Sardinia microplate. Nature 235:103-105.
5. ALVAREZ, W. 1974. Sardinia and Corsica one microplate or two? Rendiconti del Seminario della Facoltà di Scienze dell'Università di Cagliari. Libreria Cocco, Cagliari, Italy.
6. ALVAREZ, W., F. G. FRANKS, AND A. E. M. NAIRN. 1973. Paleomagnetism of Plio-Pleistocene basalts from N. W. Sardinia. Nature 243:10-11.
7. ARNTZEN, J. W., AND M. SPARREBOOM. 1989. A phylogeny of the Old World newts, genus Triturus: Biochemical and behavioural data. J. Zool. (Lond.) 219: 645-664.
8. AVISE, J. C., B. W. BOWEN, T. LAMB, A. B. MEYLAN, AND E. BERMINCHAM. 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.
9. BELLON, H., C. COULON, AND J. B. EDEL. 1977. Le déplacement de la Sardaigne synthèse des donnees géochronologiques, magmatiques et paléomagnétiques. Bull. Soc. Geol. Fr. 7:825-831.
10. BOLKAY, S. J. 1928. Die Schadel der Salamandriden mit besonderer Rucksicht auf ihre systematische Bedeutung. Z. Anat. Entwicklungsgesch. 86:259-319.
11. BONIN, B., P. CHOTIN, A. GIRET, AND J.-B. ORSINI. 1979. Étude du bloc corso-sarde sur documents satellites: Le problème des mouvements différentiels entre les deux iles. Rev. Geog. Phys. Geol. Dynam. 21:147-154.
12. BOWEN, B. W., W. S. NELSON, AND J. C. AVISE. 1993. A molecular phylogeny for marine turtles: Trait mapping, rate assessment, and conservation relevance. Proc. Natl. Acad. Sci. USA 90:5574-5577.
13. BRITTEN, R. J. 1986. Rates of DNA sequence evolution differ between taxonomic groups. Science 231:1393-1398.
14. BROWER, A. V. Z., AND R. DESALLE. 1994. Practical and theoretical considerations for choice of a DNA sequence region in insect molecular systematics, with a short review of published studies using nuclear gene regions. Ann. Entomol. Soc. Am. 87:702-716.
15. BROWN, W. M., M. GEORGE, JR., AND A. C. WILSON. 1979. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76:1967-1971.
16. BROWN, W. M., E. M. PRAGER, A. WANG, AND A. C. WILSON. 1982. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J. Mol. Evol. 18:225-239.
17. BUCCI-INNOCENTI, S., D. LACIALFARI, M. RAGGHIANTI, AND G. MANCINO. 1978. The karyotype of the Corsican and Sardinian mountain salamanders, Euproctus montanus and E. platycephalus (Urodela, Salamandridae). Experientia 34:1001-1004.
18. BULMER, M., K. H. WOLFE, AND P. M. SHARP. 1991. Synonymous nucleotide substitution rates in mammalian genes: Implications for the molecular clock and the relationship of mammalian orders. Proc. Natl. Acad. Sci. USA 88:5974-5978.
19. BUSACK, S. D., B. G. JERICHO, L. R. MAXSON, AND T. UZZELL. 1988. Evolutionary relationships of salamanders in the genus Triturus: The view from immunology. Herpetologica 44:307-316.
20. CACCONE, A., M. C. MILINKOVITCH, V. SBORDONI, AND J. R. POWELL. 1994. Molecular biogeography: Using the Corsica-Sardinia microplate disjunction to calibrate mitochondrial rDNA evolutionary rates in mountain newts (Euproctus). J. Evol. Biol. 7:227-245.
21. CANTATORE, P., M. ROBERTI, G. PESOLE, A. LUDOVICO, F. MILLELLA, M. N. GADALETA, AND C. SACCONE. 1994. Evolutionary analysis of cytochrome b sequences in some Perdformes: Evidence for a slower rate of evolution than in mammals. J. Mol. Evol. 39: 589-597.
22. CHERCHI, A., AND L. MONTADERT. 1982. Oligo-Miocene rift of Sardinia and the early history of the western Mediterranean basin. Nature 298:736-739.
23. ESTES, R. 1981. Gymnophiona, Caudata. Encycl. Paleoherpetol. 2:1-115.
24. ESU, D., AND T. KOTSAKIS. 1983. Les vertebres et les mollusques continentaux du Tertiarire de la Sardaigne: Paleobiogeographie et biostratigraphie. Geol. Rom. 22:177-206.
25. FARRIS, J. S. 1970. Methods for computing Wagner trees. Syst. Zool. 18:374-385
26. FELSENSTEIN, J. 1981. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 17:368-376.
27. FELSENSTEIN, J. 1985. Confidence limits on phytogenies: An approach using the bootstrap. Evolution 39:783-791.
28. FELSENSTEIN, J. 1993. PHYLIP: Phylogenetic inference package, version 3.5 Department of Genetics, Univ. Washington, Seattle.
29. GIACOMA, C., AND E. BALLETIO. 1988. Phylogeny of the salamandrid genus Triturus. Boll. Zool. 55:337-360.
30. GRAYBEAL, A. 1993. The phylogenetic utility of cytochrome b: Lessons from bufonid frogs. Mol. Phylogenet. Evol. 2:256-269.
31. HALLIDAY, T. R. 1977. The courtship of European newts: An evolutionary perspective. Pages 185-232 in The reproductive biology of amphibians (D. H. Taylor and S. I. Guttman, eels.). Plenum, New York.
32. HALLIDAY, T., AND B. ARANO. 1991. Resolving the phylogeny of the European newts. Trends Ecol. Evol. 6:113-117.
33. HEDGES, S. B., R. L. BEZY, AND L. R. MAXSON. 1991. Phylogenetic relationships and biogeography of xantusiid lizards, inferred from mitocnondrial DNA sequences. Mol. Biol. Evol. 8:767-780.
34. HEDGES, S. B., J. P. BOGART, AND L. R. MAXSON. 1992. Ancestry of unisexual salamanders. Nature 356: 708-710.
35. HENDY, M. D., AND D. PENNY. 1982. Branch and bound algorithms to determine minimal evolutionary trees. Math. Biosci. 59:277-290.
36. HICKSON, R., C. SIMON, A. COOPER, G. S. SPICER, J. SULLIVAN, AND D. PENNY. 1996. Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S. Mol. Biol. Evol. 13:150-169.
37. HILLIS, D. M., AND M. T. DIXON. 1991. Ribosomal DNA: Molecular evolution and phylogenetic inference. Q. Rev. Biol. 66:411-453.
38. HILLIS, D. M., B. K. MABLE, AND C. MORITZ. 1996. Applications of molecular systematics: The state of the field and a look to the future. Pages 515-543 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer, Sunderland, Massachusetts.
39. HIXSON, J. E., AND W. M. BROWN. 1986. A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: Sequence, structure, evolution, and phylogenetic information. Mol. Biol. Evol. 3:1-18.
40. IRWIN, D. M., T. D. KOCHER, AND A. C. WILSON. 1991. Evolution of the cytochrome b gene in mammals. J. Mol. Evol. 32:128-144.
41. JAYLET, A. 1966. Le caryotype de l'amphibien urodèle Euproctus asper (Duges). Chromosoma 18:79-87.
42. JUKES, T. H., AND C. CANTOR. 1969. Evolution of protein molecules. Pages 21-123 in Mammalian protein metabolism (H. N. Munro, ed.). Academic Press, New York.
43. KALEZIC, M. L., AND D. HEDGECOCK. 1980. Genetic variation and differentiation of three common European newts (Triturus) in Yugoslavia. Br. J. Herpetol. 6:49-57.
44. KLUGE, A. G., AND J. S. FARRIS. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18:1-32.
45. KNOWLTON, N., L. A. WEIGT, L. A. SOLORZANO, D. K. MILLS, AND E. BERMINGHAM. 1993. Divergence in proteins, mitochondrial DNA, and reproductive compatibility across the Isthmus of Panama. Science 260:1629-1632.
46. KOCHER, T. D., W. K. THOMAS, A. MEYER, S. V. EDWARDS, S. PÄÄBO, F. X. VILLABLANCA, AND A. C. WILSON. 1989. Dynamics of mitochondrial DNA evolution in mammals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA 86:6196-6200.
47. KRAUS, F., AND M. M. MIYAMOTO. 1991. Rapid cladogenesis among the pecoran ruminants: Evidences from mitochondrial DNA sequences. Syst. Zool. 40: 117-130.
48. LARSON, A. 1994. The comparison of morphological and molecular data m phylogenetic systematics. Pages 371-390 in Molecular ecology and evolution: Approaches and applications (B. Schierwater, B. Streit, G. P. Wagner, and R. DeSalle, eds.). Birkhäuser Verlag, Basel.
49. Li, W.-H., D. L. ELLSWORTH, J. KRUSHKAL, B. H.-J. CHAMG, AND D. HEWETT-EMMETT. 1996. Rates of nucleotide substitution in primates and rodents and the generation-time effect hypothesis. Mol. Phylogenet. Evol. 5:182-187.
50. LI, W.-H., C.-C. LUO, AND C.-I WU. 1985. Evolution of DNA sequences. Pages 1-94 in Molecular evolutionary genetics (R. J. MacIntyre, ed.). Plenum, New York.
51. MACGREGOR, H. C., S. K. SESSIONS, AND J. W. ARNTZEN. 1990. An integrative analysis of phylogenetic relationships among newts of the genus Triturus (family Salamandridae), using comparative biochemistry, cytogenetics and reproductive interactions. J. Evol. Biol. 3:329-373.
52. MADDISON, W. P., M. J. DONOGHUE, AND D. R. MADDISON. 1984. Outgroup analysis and parsimony. Syst. Zool. 33:83-103.
53. MARSHALL, C. R. 1990. The fossil record and estimating divergence times between lineages: Maximum divergence times and the importance of reliable phylogenies. J. Mol. Evol. 30:400-408.
54. MARTIN, A. P. 1995a. Mitochondrial DNA sequence evolution in sharks: Rates, patterns, and phylogenetic inferences. Mol. Biol. Evol. 12:1114-1123.
55. MARTIN, A. P. 1995b. Metabolic rate and directional nucleotide substitutions in animal mitochondrial DNA. Mol. Biol. Evol 12:1124-1131.
56. 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.
57. MARTIN, A. P., AND S. R. PALUMBI. 1993. Body size, metabolic rate, generation time, and the molecular clock. Proc. Natl. Acad. Sci. USA 90:4087-4091.
58. MEYER, A. 1993. Involution of mitochondrial DNA in fishes. Pages 1-38 in The biochemistry and molecular biology of fishes, Volume 2 (P. W. Hochachka and T. P. Mommsen, eds.). Elsevier, Amsterdam.
59. MEYER, A., AND A. C. WILSON. 1990. Origin of tetrapods inferred from their mitochondrial DNA affiliation to lungfish. J. Mol. Evol. 31:359-364.
60. MILINKOVITCH, M. C., G. ORTÍ, AND A. MEYER. 1995. Novel phylogeny of whales revisited but not revised. Mol. Biol. Evol. 12:518-520.
61. MINDELL, D., AND R. L. HONEYCUTT. 1990. Ribosomal RNA: Evolution and phylogenetic applications. Annu. Rev. Ecol. Syst. 21:541-566.
62. MIYAMOTO, M. M. AND S. M. BOYLE. 1989. The potential importance of mitochondrial DNA sequence data to eutherian mammal phylogeny. Pages 437-450 in The hierarchy of life (B. Fernholm, K. Bremer, and H. Jörnvall, eds.). Elsevier, Amsterdam.
63. MORITZ, C., AND W. M. BROWN. 1986. Tandem duplications of D-loop and ribosomal RNA sequences in lizard mitochondrial DNA. Science 233:1425-1427.
64. MORITZ, C., AND W. M. BROWN. 1987. Tandem duplications in animal mitochondrial DNAs: Variation in incidence and gene content among lizards. Proc. Natl. Acad. Sci. USA 84:7183-7187.
65. MORITZ, C., T. E. DOWLING, AND W. M. BROWN. 1987. Evolution of animal mitochondrial DNA: Relevance for population biology and systematics. Annu. Rev. Ecol. Syst. 18:269-292.
66. MORITZ, C., C. J. SCHNEIDER, AND D. B. WAKE. 1992. Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Syst. Biol. 41:273-291.
67. MUSE, S. V., AND B. S. WEIR. 1992. Testing for equality of evolutionary rates. Genetics 132:269-276.
68. OOSTERBROEK, P., AND J. W. ARNTZEN. 1992. Area-cladograms of circum-Mediterranean taxa in relation to Mediterranean paleogeography. J. Biogeogr. 19:3-20.
69. ORSINI, J. B., C. COULON, AND T. COCOZZA. 1980. La dérive cénozoique de la Corse et de la Sardaigne. Géol. Alp. 56:169-202.
70. ORTÍ, G., P. PETRY, J. I. R. PORTO, M. JÈGU, AND A. MEYER. 1996. Patterns of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas. J. Mol. Evol. 42:169-182.
71. PÄÄBO, S. 1990. Amplifying ancient DNA. Pages 159-166 in PCR protocols, a guide to methods and applications (M. A. Innis, D. H. Gelfand, J. J. Sninsky, and T. J. White, eds.). Academic Press, New York.
72. PALUMBI, S., A. MARTIN, S. ROMANO, W. O. MCMILLAN, L. STICE, AND G. GRABOWSKI. 1991. The simple fool's guide to PCR, version 2.0. Univ. Hawaii, Honolulu.
73. POWELL, J. R., A. CACCONE, G. D. AMATO, AND C. YOON. 1986. Rates of nucleotide substitutions in Drosophila mitochondrial DNA and nuclear DNA are similar. Proc. Natl. Acad. Sci. USA 83:9090-9093.
74. RAFINSKI, J., AND J. W. ARNTZEN. 1987. Biochemical systematics of the Old World newts Triturus: Allozyme data. Herpetologica 43:446-457.
75. RAND, D. M. 1994. Thermal habit, metabolic rate, and the evolution of mitochondrial DNA. Trends Ecol. Evol. 9:125-131.
76. REEDER, T. W. 1995. Phylogenetic relationships among phrynosomatid lizards as inferred from mitochondrial ribosomal DNA sequences: Substitutional bias and information content of transitions relative to transversions. Mol. Phylogenet. Evol. 4:203-222.
77. RITCHIE, P. A., L. BARGELLONI, A. MEYER, J. A. TAYLOR, J. A. MACDONALD, AND D. M. LAMBERT. 1996. Mitochondrial phylogeny of trematomid fishes (Nototheniidae, Perciformes) and the evolution of Antarctic fish. Mol. Phylogenet. Evol. 5:383-390.
78. SAITOU, N., AND M. NEI. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
79. SANDERSON, M. J., AND M. J. DONOGHUE. 1989. Patterns of variation in levels of homoplasy. Evolution 43:1781-1795.
80. SARICH, V. M., AND A. C. WILSON. 1967. Rates of albumin evolution in primates. Proc. Natl. Acad. Sci. USA 58:142-148.
81. SBORDONI, V., A. CACCONE, G. ALLEGRUCCI, AND D. CESARONI. 1990. Molecular island biogeography. Pages 55-83 in Biogeographical aspects of insularity, Atti dei Convegni Lincei, Volume 85 (A. Azzaroli, ed.). Accademia Nazionale dei Lincei, Roma.
82. SIMON, C., F. FRATI, A. BECKENBACH, B. CRESPI, H. LIU, AND P. FLOOK. 1994. Evolution, weighting and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87:651-701.
83. SIMON, C., L. NIGRO, J. SULLIVAN, K. HOLSINGER, A. MARTIN, A. GRAPPUTO, A. FRANKE, AND C. MCINTOSH. 1996. Large differences in substitutional patterns and evolutionary rate of the 12S ribosomal RNA genes. Mol. Biol. Evol. 13:923-932.
84. SMITH, A. B. 1994. Rooting molecular trees: Problems and strategies. Biol. J. Linn. Soc. 51:279-292.
85. SMITH, M. F., W. K. THOMAS, AND J. L. PATTON. 1992. Mitochondrial DNA-like sequence in the nuclear genome of an akodontine rodent. Mol. Biol. Evol. 9: 204-215.
86. SPOLSKY, C. M., C. A. PHILLIPS, AND T. UZZELL. 1992. Antiquity of clonal salamander lineages revealed by mitochondrial DNA. Nature 356:706-708.
87. SPRINGER, M. S., AND J. A. W. KIRSCH. 1989. Rates of single-copy DNA evolution in phalangeriform marsupials. Mol. Biol. Evol. 6:331-341.
88. SULLIVAN, J., K. E. SULLIVAN, AND C. SIMON. 1995. Among-site rate variation and phylogenetic analysis of the 12S rRNA in sigmodontine rodents. Mol. Biol. Evol. 12:988-1001.
89. SWOFFORD, D. 1993. PAUP: Phylogenetic analysis using parsimony, version 3.1.1s. Illinois Natural History Survey, Champaign.
90. TAJIMA, F. 1993. Simple methods for testing the molecular evolutionary clock hypothesis. Genetics 135: 599-607.
91. TAKAHATA, N., AND M. KIMURA. 1981. A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics 98:641-657.
92. TAN, A.-M., AND D. WAKE. 1995. MtDNA phylogeography of the California newt Taricha torosa (Caudata, Salamandridae). Mol. Phylogenet. Evol. 4:383-394.
93. TEMPLETON, A. 1983. Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37:221-244.
94. THIESMAIER, B., AND C. HORNBERG. 1990. Zur Fortpflanzung sowie zum Paarungsverhalten der Gebirgsmolche, Gattung Euproctus (Genè), im Terrarium, unter besonderer Berucksichtigung von Euproctus asper (Duges, 1852). Salamandra 26:63-82.
95. THORN, R. 1968. Les salamandres d'Europe, d'Asie et d'Afrique du Nord. Lechevalier, Paris.
96. TITUS, T. A., AND A. LARSON. 1995. A molecular phylogenetic perspective on the evolutionary radiation of the salamander family Salamandridae. Syst. Biol. 44:125-151.
97. VAWTER, L., AND W. M. BROWN. 1986. Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock. Science 234: 194-196.
98. VAWTER, L., AND W. M. BROWN. 1993. Rates and patterns of base changes in the small subunit ribosomal RNA gene. Genetics 134:597-608.
99. VAN DE PEER, Y., J.-M. NEEFS, P. DE RIJK, AND R. DE WACHTER. 1993. Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences: Calibration of the molecular clock. J. Mol. Evol. 37: 221-232.
100. WAKE, D. B., AND N. OZETI. 1969. Evolutionary relationships in the family Salamandridae. Copeia 1969: 124-137.
101. WALLIS, G. P. 1987. Mitochondrial DNA insertion polymorphism and germ line heteroplasmy in the Triturus cristatus complex. Heredity 58:229-238.
102. WALLIS, G. P., AND J. W. ARNTZEN. 1989. Mitochondrial DNA variation in the crested newt superspecies: Limited cytoplasmic gene flow among species. Evolution 43:88-104.
103. WATROUS, L. E., AND Q. D. WHEELER. 1981. The outgroup comparison method of character analysis. Syst. Zool. 30:1-11.
104. WHEELER, W. C., AND D. GLADSTEIN. 1993. MALIGN, version 1.5. American Museum of Natural History, New York.
105. WU, C.-I., AND W.-H. LI. 1985. Evidence for higher rates of nucleotide substitution in rodents than in men. Proc. Natl. Acad. Sci. USA 82:1741-1745.
106. ZHANG, Y., AND O. RYDER. 1995. Different rates of mitochondrial DNA sequences evolution in Kirk's dik-dik (Madoqua kirkii) populations. Mol. Phylogenet. Evol. 4:291-297.
107. ZUCKERKANDL, E., AND L. PAULING. 1965. Evolutionary divergence and convergence in proteins. Pages 97-166 in Evolving genes and proteins (V. Bryson and H. J. Vogel, eds.). Academic Press, New York.