Journal of Molecular Evolution

, Volume 42, Issue 2, pp 169–182 | Cite as

Patterns of nucleotide change in mitochondrial ribosomal RNA genes and the phylogeny of piranhas

  • Guillermo Ortí
  • Paulo Petry
  • Jorge I. R. Porto
  • Michel Jégu
  • Axel Meyer


The patterns and rates of nucleotide substitution in mitochondrial ribosomal RNA genes are described and applied in a phylogenetic analysis of fishes of the subfamily Serrasalminae (Teleostei, Characiformes, Characidae). Fragments of 345 bp of the 12S and 535 bp of the 16S genes were sequenced for 37 taxa representing all but three genera in the subfamily. Secondary-structure models based on comparative sequence analysis were derived to characterize the pattern of change among paired and unpaired nucleotides, forming stem and loop regions, respectively. Base compositional biases were in the direction of A-rich loops and G-rich stems. Ninety-five percent of substitutions in stem regions were compensatory mutations, suggesting that selection for maintenance of base pairing is strong and that independence among characters cannot be assumed in phylogenetic analyses of stem characters. The relative rate of nucleotide substitution was similar in both fragments sequenced but higher in loop than in stem regions. In both genes, C-T transitions were the most common type of change, and overall transitions outnumbered transversions by a factor of two in 16S and four in 12S. Phylogenetic analysis of the mitochondrial DNA sequences suggests that a clade formed by the generaPiaractus, Colossoma, andMylossoma is the sister group to all other serrasalmins and that the generaMyleus, Serrasalmus, andPristobrycon are paraphyletic. A previous hypothesis concerning relationships for the serrasalmins, based on morphological evidence, is not supported by the molecular data. However, phylogenetic analysis of host-specific helminth parasites and cytogenetic data support the phylogeny of the Serrasalminae obtained in this study and provide evidence for coevolution between helminth parasites and their fish hosts.

Key words

Mitochondrial rRNA sequences rRNA secondary structure Molecular phylogeny Serrasalminae Coevolution 


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  1. Adachi J, Hasegawa M (1994) MOLPHY: a program package for molecular phylogenetics, version 2.2. The Institute of Statistical Mathematics, TokyoGoogle Scholar
  2. Alves-Gomes JA, Ortí G, Haygood M, Heiligenberg W, Meyer A (1995) Phylogenetic analysis of the South American electric fishes (Order Gymnotiformes) and the evolution of their electrogenic system: a synthesis based on morphology, electrophysiology, and mitochondrial sequence data. Mol Biol Evol 12:298–318Google Scholar
  3. Anderson S, Bankier AT, Barrell BG, de Brujin MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465Google Scholar
  4. Aquadro CF, Greenberg BD (1983) Human mitochondrial DNA variation and evolution: analysis of nucleotide sequences from seven individuals. Genetics 103:287–312Google Scholar
  5. Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18:225–239Google Scholar
  6. Cestari MM, Galetti Jr PM (1992) Chromosome evolution in the genusSerrasalmus and cytotaxonomic considerations about Serrasalminae (Characidae, Pisces). Rev Brasil Genet 15:555–567Google Scholar
  7. Collins TM, Wimberger PH, Naylor GJP (1994) Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst Biol 43:482–496Google Scholar
  8. Dams E, Hendriks L, Van de Peer Y, Neefs JM, Smits G, Vandenbempt I, De Wachter R (1988) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 16s:r87-r173Google Scholar
  9. Dixon MT, Hillis DM (1993) Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis. Mol Biol Evol 10:256–267Google Scholar
  10. Eigenmann C (1915) The Serrasalminae and Mylinae. Ann Carnegie Museum, Pittsburgh 9:266–272Google Scholar
  11. Farris JS (1969) A successive approximations approach to character weighting. Syst Zool 18:374–385Google Scholar
  12. Felsenstein J (1969) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376Google Scholar
  13. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791Google Scholar
  14. Fink WL (1993) Revision of the piranha genusPygocentrus (Teleostei, Characiformes). Copeia 1993:665–687Google Scholar
  15. Fitch WM, Markowitz E (1970) An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet 4:579–593Google Scholar
  16. Géry J (1972) Poissons characoides des Guyanes II. Famille des Serrasalmidae. Zoologische Verhandelingen Leiden 122:134–248Google Scholar
  17. Géry J (1977) Characoids of the World. Tropical Fish Hobbyist Publications, Neptune City, NJ, pp 672Google Scholar
  18. Gosline W (1951) Notes on the characoid fishes of the Subfamily Serrasalminae. Proc Cal Acad Sci, ser 4 27:17–64Google Scholar
  19. Goulding M (1980) The fishes and the forest. Explorations in Amazonian natural history. University of California Press, Berkeley, p 280Google Scholar
  20. Gray MW, Cedergren R (1993) The new age of RNA. FASEB J 7:4–6Google Scholar
  21. Guttel RR, Fox GE (1988) A compilation of large subunit rRNA sequences presented in a structural format. Nucleic Acids Res 16s:r175-r269Google Scholar
  22. Guttel RR, Gray MW, Schare MN (1993) A compilation of large subunit 23S and 23S-like) ribosomal RNA structures: 1993. Nucleic Acids Res 21:3055–3074Google Scholar
  23. Guttel RR, Weiser B, Woese CR, Noller HF (1985) Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol 32:155–216Google Scholar
  24. Gyllensten UB, Erlich HA (1988) Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQa locus. Proc Natl Acad Sci USA 85:7652–7655Google Scholar
  25. Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Q Rev Biol 66:411–453Google Scholar
  26. Hixon JE, Brown WM (1986) A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: sequence, structure, evolution and phylogenetic implications. Mol Biol Evol 3:1–18Google Scholar
  27. Jégu M, Tito de Morais L, Mendes dos Santos G (1992) Redescription des types d′Utiaritichthys sennaebragai Miranda Ribeiro, 1937 et description d'une nouvelle espéce du bassin Amazonien, (Characiformes, Serrasalmidae). Cybium 16:105–120Google Scholar
  28. Junk WJ (1984) Ecology, fisheries and fish culture in Amazonia. In: Sioli H (ed) The Amazon, limnology and landscape ecology of a mighty tropical river and its basin. Dr. W. Junk Publishers, Dordrecht, pp 443–476Google Scholar
  29. Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458Google Scholar
  30. Kishino H, Hasegawa M (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. J Mol Evol 29:170–179Google Scholar
  31. Kocher TD, Thomas WK, Meyer A, Edwards SV, Pääbo S, Villablanca FX, Wilson AC (1989) Dynamics of mitochondrial DNA evolution in animals. Proc Natl Acad Sci USA 86:6196–6200Google Scholar
  32. Kumar S, Tamura K, Nei M (1993) MEGA: molecular evolutionary genetics analysis, version 1.0. The Pennsylvania State University, University Park, PAGoogle Scholar
  33. Larson A, Wilson AC (1989) Patterns of ribosomal RNA evolution in salamanders. Mol Biol Evol 6:131–154Google Scholar
  34. Lee W, Kocher TD (1995) Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. Genetics 139:873–887Google Scholar
  35. Leite RG, Jégu M (1990) Food habits of two species ofAcnodon (Characiformes, Serrasalmidae) and scale-eating habits ofAcnodon normani. Cybium 14:353–360Google Scholar
  36. Lundberg JG (1993) African-South American freshwater fish clades and continental drift: problems with a paradigm. In: Goldblatt P (ed) Biological relationships between African and South America. Yale University Press, New Haven, pp 156–199Google Scholar
  37. Lundberg JG, Machado-Allison A, Kay RF (1986) Miocene characid fishes from Colombia: evolutionary stasis and extirpation. Science 234:208–209Google Scholar
  38. Machado-Allison A (1982) Studies on the systematics of the subfamily Serrasalminae (Pisces-Characidae). Unpublished PhD thesis, The George Washington University, Washington DCGoogle Scholar
  39. Machado-Allison A (1983) Estudios sobre la sistemática de la subfamilia Serrasalminae (Teleostei, Characidae), parte II. Discusión sobre la condición monofilética de la subfamilia. Acta Biol Venez 11:145–195Google Scholar
  40. Machado-Allison A, Fink WL, Antonio ME (1989) Revisión del géneroSerrasalmus Lacepede, 1803 y géneros relacionados en Venezuela: I. Notas sobre la morfología y sistemática dePristobrycon striolatus (Steindachner, 1908). Acta Biol Venez 12:140–171Google Scholar
  41. Maddison WP, Maddison DR (1992) MacCLADE: analysis of phylogeny and character evolution, version 3.0. Sinauer, Sunderland, MAGoogle Scholar
  42. Maniatis T, Fritsch EF, Sambrook J (1982) Molecular cloning: a laboratory manual. Cold Spring Harbor Publications, Cold Spring Harbor, NYGoogle Scholar
  43. Marshall E (1995) Homely fish draws attention to Amazon deforestation. Science 267:814Google Scholar
  44. Meyer A (1993) Evolution of mitochondrial DNA of fishes. In: Hochachka PW, Mommsen P (eds) The biochemistry and molecular biology of fishes, vol 2. Elsevier Press, Amsterdam, pp 1–38Google Scholar
  45. Meyer A (1994) DNA technology and phylogeny of fish. In: Beaumont AR (ed) Genetics and evolution of aquatic organisms. Chapman and Hall, London pp. 219–249Google Scholar
  46. Mindell DP, Honeycutt RL (1990) Ribosomal RNA in vertebrates: evolution and phylogenetic implications. Annu Rev Ecol Syst 21:541–566Google Scholar
  47. Neefs JM, Van de Peer Y, De Rijk P, Goris A, De Wachter R (1991) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res 19s:1987–2015Google Scholar
  48. Nelson EM (1961) The swim bladder in the Serrasalminae, with notes on additional morphological features. Fieldiana Zool 39:603–624Google Scholar
  49. Nico L, Taphorn DC (1988) Food habits of piranhas in the low Ilanos of Venezuela. Biotropica 20:311–321Google Scholar
  50. Noller HF (1984) Structure of ribosomal RNA. Annu Rev Biochem 53:119–162Google Scholar
  51. Norman JR (1929) The South American Characid fishes of the subfamily Serrasalmoninae with a revision of the genusSerrasalmus Lacepede. Proc Zool Soc London 52:661–1044Google Scholar
  52. Oliveira C, Almeida-Toledo LF, Foresti F, Britski H, Toledo-Filho SA (1988) Chromosome formulae of Neotropical freshwater fishes. Rev Bras Genet 11:577–624Google Scholar
  53. Olsen GJ, Matsuda H, Hagstrom R, Overbeek R (1994) fast DNAml: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci 10:41–48Google Scholar
  54. Olsen GJ, Woese CR (1993) Ribosomal RNA: a key to phylogeny. FASEB J 7:113–123Google Scholar
  55. Ortí G (1995) Molecular systematics of characiform fishes. Unpublished PhD thesis, State University of New York at Stony BrookGoogle Scholar
  56. Ortí G, Meyer A (1996) The radiation of characiform fishes and the limits of resolution of mitochondrial ribosomal DNA sequences. Syst Biol 45(in press)Google Scholar
  57. Palumbi S, Martin A, Romano S, McMillan WO, Stice L, Grabowski G (1991) The simple fool's guide to PCR. Dept of Zoology and Kewalo Marine Laboratory, University of Hawaii, HonoluluGoogle Scholar
  58. Porto JIR, Feldberg E, Nakayama C, Falcao JN (1992) A checklist of chromosome numbers and karyotypes of Amazonian freshwater fishes. Rev Hydrobiol Trop 25:287–299Google Scholar
  59. Porto JIR, Feldberg E, Nakayama CM, Jégu M (1989) Análise cariotípica na familia Serrasalmidae (Ostariophysi, Characiformes): aspectos evolutivos. Ciencia é Cultura (Suppl) 41:714Google Scholar
  60. Porto JIR, Feldberg E, Nakayama CM, Maia RO, Jégu M (1991) Cytotaxonomic analysis in the Serrasalmidae (Ostariophysi, Characiformnes). VIII Congress of Ichthylogy. Bull Zool Mus Univ, Amsterdam, The HagueGoogle Scholar
  61. Saiki RK, Gelfand DH, Stoffel S, Scharf S, Higuchi R, Horn GT, Mullis KB, Erlich HA (1988) Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491Google Scholar
  62. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–525Google Scholar
  63. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain terminator inhibitors. Proc Natl Acad Sci USA 74:5436–5437Google Scholar
  64. Schimmel PR, Soll D, Abelson JN (1979) Transfer RNA: structure, properties and recognition. Cold Spring Harbor Laboratory, Cold Spring Harbor, NYGoogle Scholar
  65. Swofford DL (1993) PAUP: Phylogenetic Analysis Using Parsimony, ver 3.1.1. Smithsonian Institution, Washington, DCGoogle Scholar
  66. Swofford DL, Maddison WP (1992) Parsimony, character-state reconstructions, and evolutionary inferences. In: Mayden RL (ed) Systematics, historical ecology, and North American freshwater fishes. Stanford University Press, Stanford, pp 186–223Google Scholar
  67. Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular systematics. Sinauer, Sunderland MA, pp 411–501Google Scholar
  68. Thompson JD, Higgins DG, Gibson TJ (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 22:4673–4680Google Scholar
  69. Turner DH, Sugimoto N, Freier SM (1988) RNA structure prediction. Annu Rev Biophys Chem 17:167–192Google Scholar
  70. Tzeng CS, Hui CF, Shen SC, Huang PC (1992) The complete nucleotide sequence of theCrossostoma lacustre mitochondrial genome: conservation and variations among vertebrates. Nucleic Acids Res 20:4853–4858Google Scholar
  71. Van Every LR, Kritsky DC (1992) Neotropical Monogenoida. 18.Anacanthorus Mizelle and Price, 1965 (Dactylogyridae, Anacanthorinae) of piranha (Characoidea, Serrasalmidae) from the central Amazon, their phylogeny, and aspects of host-parasite coevolution. J Helminthol Soc Wash 59:52–75Google Scholar
  72. Vawter L, Brown WM (1993) Rates and patterns of base change in the small subunit ribosomal RNA gene. Genetics 134:597–608Google Scholar
  73. Wheeler WC, Honeycutt RL (1988) Paired sequence difference in ribosomal RNAs: evolutionary and phylogenetic implications. Mol Biol Evol 5:90–96Google Scholar
  74. Winemiller KO (1989) Ontogenetic diet shifts and resource partitioning among piscivorous fishes in the Venezuelan Llanos. Environ Biol Fishes 26:177–199Google Scholar
  75. Wolstenholme DR, Clary DO (1985) Sequence evolution ofDrosophila mitochondrial DNA. Genetics 109:725–744Google Scholar
  76. Zardoya R, Garrido-Pertierra A, Bautista JM (1995) The complete nucleotide sequence of the mitochondrial DNA genome of the rainbow trout,Oncorhynchus mykiss. J Mol Evol 41:(in press)Google Scholar

Copyright information

© Springer-Verlag New York Inc. 1996

Authors and Affiliations

  • Guillermo Ortí
    • 1
  • Paulo Petry
    • 2
  • Jorge I. R. Porto
    • 2
  • Michel Jégu
    • 2
    • 3
  • Axel Meyer
    • 1
    • 4
  1. 1.Department of Ecology and EvolutionState University of New York at Stony BrookStony BrookUSA
  2. 2.Instituto Nacional de Pesquisas da Amazonia (INPA/CPBA), CxP 478, CEP 69Manaus, AMBrazil
  3. 3.Départment Des Eaux ContinentalesORSTOMParis Cedex 10France
  4. 4.Program in GeneticsState University of New York at Stony BrookStony BrookUSA

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