Reviews in Fish Biology and Fisheries

, Volume 21, Issue 4, pp 779–788 | Cite as

5S rDNA chromosomal mapping and COI sequence analysis reveal differentiation among distinct populations of a characid fish Serrapinnus notomelas

  • T. C. Mariguela
  • L. R. S. Paiva
  • F. Foresti
  • C. Oliveira
Research paper


Cheirodontinae comprises a small-sized fish group with a wide geographical distribution throughout Central and South America, mainly in Brazilian Basins. The species Serrapinnus notomelas is widely distributed in the Upper Parana River Basin. In this work, chromosomal mapping of 5S ribosomal RNA (rRNA) gene was performed trough fluorescence in situ hybridization (FISH) in speciemens from three distinct localities belonging to two basins in the São Paulo State. All populations presented 5S clusters in two chromosome pairs. One additional pair was detected in samples from the Rio Paraitinguinha (Tietê Basin), and two additional pairs were detected in the population from Córrego Campo Novo (Tietê Basin). Analyses with partial sequences of COI were performed to verify the interelationship among the studied specimens, revealing Córrego Campo Novo population as a sister-group to the clade formed by the two other populations. The samples from Rio Paraitinguinha and Recanto dos Cambarás presented two distinct haplotypes each, while five haplotypes were observed in the Córrego Campo Novo population, sugesting that this could be older than the other populations. None of the nine haplotypes were shared among the three populations. The similarities and differences observed among the three populations using cytogenetic data and COI analysis are not related to geographic distances that separate the samples, suggesting that the origin of the Rio Paraitinguinha and Recanto dos Cambarás populations may be related to faunal exchanges. Additionally, the present data suggest that the analyzed populations of S. notomelas may be on independent evolutionary trajectories but in a very initial diversification stage. Moreover, the use of integrative information, such as molecular and chromosomal data in the analysis of population divergence and evolutionary trajectories in freshwater fishes is reinforced.


Cheirodontinae Chromosome polymorphism Cytochrome oxidase I Fluorescence in situ hybridization Haplotypes Mitochondrial gene 



We are grateful to Renato Devidé for his help with fish collection and Luiz Roberto Malabarba for his help with fish identification. This research was supported by FAPESP (Fundação de Amparo à Pesquisa do Estado de São Paulo) and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico).


  1. Akaike H (1974) A new look at the statistical model indentification. IEEE Trans Automat Contr 19:716–722CrossRefGoogle Scholar
  2. Aljanabi SM, Martinez I (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res 25:4692–4693PubMedCrossRefGoogle Scholar
  3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  4. Benine RC, Mariguela TC, Oliveira C (2009) New species of Moenkhausia Eigenmann, 1903 (Characiformes: Characidae) with comments on the Moenkhausia oligolepis speciess complex. Neotrop Ichthyol 7:161–168CrossRefGoogle Scholar
  5. Carrera E, García T, Céspedes A, González I, Frenández A, Asensio LM, Hernández PE, Martín R (2000) Differentiation of smoked Salmo salar, Oncorhynchus mykiss and Brama raii using the nuclear marker 5S rDNA. Int J Food Sci Technol 35:401–406CrossRefGoogle Scholar
  6. Clement M, Posada D, Crandall KA (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9:1657–1660PubMedCrossRefGoogle Scholar
  7. Cobbold PR, Meisling KE, Mount VS (2001) Reactivation of an obliquely rifted margin, Campos and Santos basins, southeastern Brazil. Am Assoc Petrol Geol Bull 85(11):1925–1944Google Scholar
  8. Cox AJ, Hebert PDN (2001) Colonization, extinction and phylogeographic patterning in a freshwater crustacean. Mol Ecol 10:371–386PubMedCrossRefGoogle Scholar
  9. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797PubMedCrossRefGoogle Scholar
  10. Excoffier L, Schneider S (2005) Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinform 1:47–50Google Scholar
  11. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791CrossRefGoogle Scholar
  12. Ferreira I, Oliveira C, Venere PC, Galetti PM, Martins C (2007) 5S rDNA variation and its phylogenetic inference in the genus Leporinus (Characiformes: Anostomidae). Genetica 129:253–257PubMedCrossRefGoogle Scholar
  13. Foresti F, Oliveira C, Almeida-Toledo LF (1993) A method for chromossome preparations from large fish specimens using in vitro short-term treatment with colchicines. Experientia 49:810–813CrossRefGoogle Scholar
  14. Frederiksen S, Cao H, Lomholt B, Levan G, Hallemberg C (1997) The rat 5S rRNA bona fide gene repeat maps to chromosome 19q12 → qter and the pseudogene repeat maps to 12q12. Cytogen Cell Genet 76:101–106CrossRefGoogle Scholar
  15. Géry J (1977) Characoids of the world. TFH Publication, Nepture CityGoogle Scholar
  16. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98Google Scholar
  17. Hebert PDN, Cywinska A, Ball SL, de Waard JR (2003a) Biological identifications throught DNA barcodes. Proc Royal Soc B Biol Sci 270:313–322CrossRefGoogle Scholar
  18. Hebert PDN, Ratnasingham S, de Waard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proc Royal Soc B Biol Sci 270:S96–S99CrossRefGoogle Scholar
  19. Hubert N, Hanner R, Holm E, Mandrak NE, Taylor E, Burridge M, Watkinson D, Dumont P, Curry A, Bentzen P, Zhang J, April J, Bernatchez L (2008) Identifying Canadian freshwater fishes through DNA barcodes. PloS ONE 3:e2490CrossRefGoogle Scholar
  20. Huelsenbeck JP, Ronquist F (2001) MrBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17:755CrossRefGoogle Scholar
  21. Huelsenbeck JP, Ronquist F, Nielsen R, Bollback JP (2001) Bayesian inference of phylogeny and its impact of evolutionary biology. Science 294:2310–2314PubMedCrossRefGoogle Scholar
  22. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120PubMedCrossRefGoogle Scholar
  23. Long EO, David ID (1980) Repeated genes in eukaryotes. Ann Rev Biochem 49:727–764PubMedCrossRefGoogle Scholar
  24. Lucchini S, Nardi I, Barsacchi G, Batistoni R, Andronico F (1993) Molecular cytogenetics of the ribosomal (18S + 28S and 5S) DNA loci in primitive and advanced urodele amphibians. Genome 36:762–773PubMedCrossRefGoogle Scholar
  25. Maddison DR, Maddison WP (2000) MacClade 4.0: analysis of phylogeny and character evolution. Sinauer Associates Inc., SunderlandGoogle Scholar
  26. Mäkinem A, Zijlstra C, De Haan NA, Mellink CHM, Bosma AA (1997) Localization of 18S plus 28S and 5S ribosomal RNA genes in the dog by fluorescence in situ hybridization. Cytogen Cell Genet 73:149–152Google Scholar
  27. Malabarba LR (1998) Monophyly of the Cheirodontinae, characters and major clades (Ostariophysi: Characidae). In: Malabarba LR, Reis RE, Vari RP, Lucena ZM, Lucena CA (eds) Phylogeny and classification of neotropical fishes. Edipucrs, Porto Alegre, pp 193–233Google Scholar
  28. Malabarba LR (2003) Subfamily Cheirodontinae. In: Reis RE, Kullander SO, Ferraris C (eds) Check list of the fishes of South and Central America. Edipucrs, Porto Alegre, pp 215–221Google Scholar
  29. Martins C (2007) Chromosomes and repetitive DNAs: a contribution to the knowledge of fish genome. In: Pisano E, Ozouf-Costaz C, Foresti F, Kappor BG (eds) Fish cytogenetics. Science Publisher Inc., Enfield, pp 421–453Google Scholar
  30. Martins C, Galetti PM (2001a) Two 5S rDNA arrays in Neotropical fish species: is it a rule for fishes? Genetica 111:439–446PubMedCrossRefGoogle Scholar
  31. Martins C, Galetti PM (2001b) Organization of 5S rDNA in Leporinus fish species: two different genomic locations are characterized by distinct non-transcribed spacers (NTSs). Genome 44:903–910PubMedGoogle Scholar
  32. Martins C, Wasko AP (2004) Organization and evolution of 5S ribosomal DNA in the fish genome. In: Williams CR (ed) Focus on genome research. Nova Science Publishers, Hauppauge, pp 289–318Google Scholar
  33. Mellink CHM, Bosma AA, Haan NA, Zijlstra C (1996) Physical localization of 5S rRNA genes in the pig by fluorescence in situ hybridization. Hereditas 124:37–49Google Scholar
  34. Melo BF, Benine RC, Mariguela TC, Oliveira C (in press) A new species of Tetragonopterus Cuvier, 1816 (Characiformes: Characidae: Tetragonopterinae) from the Rio Jari, Amapá, northern Brazil. Neotrop IchthyolGoogle Scholar
  35. Menezes NA, Weitzman SH (1990) Two new species of Mimagoniates (Teleostei: Characidae: Glandulocaudinae), their phylogeny and biogeography and a key to the glandulocaudinae fishes of Brazil and Paraguay. Proc Biol Soc Wash 103(2):380–426Google Scholar
  36. Morán P, Martinez JL, Garcia-Vásquez E, Pendás AM (1996) Sex linkage of 5S rDNA in rainbow trout (Oncorhinchus mykiss). Cytogen Cell Genet 75:145–150CrossRefGoogle Scholar
  37. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
  38. Nishiyama PB, Santos IC (1995) Caracterização cromossômica de duas espécies do gênero Cheirodon (Pisces, Characidae). Rev Bras Genet 18:458Google Scholar
  39. Oliveira C, Wright JM (1998) Molecular cytogenetic analysis of heterochromatin in the chromosomes of tilapia, Oreochromis niloticus (Teleostei: Ciclidae). Chromosome Res 6:205–211PubMedCrossRefGoogle Scholar
  40. Pendás AM, Morán P, Martínez JL, García-Vazquez E (1995) Applications of 5S rDNA in Atlantic salmon, brown trout, and in Atlantic salmon x brown trout hybrid identification. Mol Ecol 4:275–276PubMedCrossRefGoogle Scholar
  41. Pinkel D, Straume T, Gray JW (1986) Cytogenetic analysis using quantitative, highsensitivity, fluorescence hybridization. Proc Nat Acad Sci USA 83:2934–2938PubMedCrossRefGoogle Scholar
  42. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol 53:793–808PubMedCrossRefGoogle Scholar
  43. Posada D, Crandall KA (1998) Modeltest: testing the model of DNA substitution. Bioinformatics 14:817–818PubMedCrossRefGoogle Scholar
  44. Ribeiro AC (2006) Tectonic history and the biogeography of the freshwater fishes from the coastal drainages of eastern Brazil: an example of faunal evolution associated with a divergent continental margin. Neotrop Ichthyol 4(2):225–246CrossRefGoogle Scholar
  45. Ribeiro AC, Lima FCT, Riccomini C, Menezes NA (2006) Fishes of the Atlantic rainforest of Boracéia: testimonies of the quaternary fault reactivation within a Neoproterozoic tectonic province in Southeastern Brazil. Ichthyol Explor Fresh 17(2):157–164Google Scholar
  46. Riccomini C, Sant’Anna LG, Ferrari AL (2004) Evolução geológica do rift continental do sudeste do Brasil. In: Mantesso-Neto V, Bartorelli A, Carneiro CDR, Brito-Neves BB (eds) Geologia do continente Sul-Americano: evolução da obra de Fernando Flávio Marques de Almeida. Editora Beca, São Paulo, pp 383–405Google Scholar
  47. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  48. Santi-Rampazzo AP, Nishiyama PB, Ferreira PEB, Martins-Santos IC (2007) Cytogenetic analysis and description of the sexual chromosome determination system ZZ/ZW of species of the fish genus Serrapinnus (Characidae, Cheirodontinae). Genet Mol Res 6:504–509PubMedGoogle Scholar
  49. Santi-Rampazzo AP, Nishiyama PB, Ferreira PEB, Martins-Santos IC (2008) Intrapopulational polymorphism of nucleolus organizer regions in Serrapinnus notomelas (Characidae, Cheirodontinae) from the Paraná River. J Fish Biol 72:1236–1243CrossRefGoogle Scholar
  50. Schmid M, Vitelli L, Batistoni R (1987) Chromosome banding in Amphibia. IV. Constitutive heterochromatin, nucleolus organizers, 18S + 28S and 5S ribosomal RNA genes in Ascaphidae, Pipidae, Discoglossidae and Pelobatidae. Chromosoma 95:271–284PubMedCrossRefGoogle Scholar
  51. Smith P, McVeagh S, Steinke D (2008) DNA barcoding for the identification of smoked fish products. J Fish Biol 72:464–471CrossRefGoogle Scholar
  52. Spies IB, Gaichas S, Stevenson DE, Orr JW, Canino MF (2006) DNA-based identification of Alaska skates (Amblyraja, Bathyraja and Raja: Rajidae) using cytochrome c oxidase subunit I (COI) variation. J Fish Biol 69:283–292CrossRefGoogle Scholar
  53. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599PubMedCrossRefGoogle Scholar
  54. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics 132:619–633PubMedGoogle Scholar
  55. Thompson JD, Higgins DG, Gibson TJ, Clustal W (1994) Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680PubMedCrossRefGoogle Scholar
  56. Valdez-Moreno M, Ivanova V, Elias-Gutierrez M, Contreras-Balderas S, Hebert PDN (2009) Probing diversity in freshwater fishes from Mexico and Guatemala with DNA barcodes. J Fish Biol 74:377–402PubMedCrossRefGoogle Scholar
  57. Vitelli L, Batistoni R, Andronico F, Nardi I, Barsacchi-Piloni G (1982) Chromosomal localization of 18S + 28S and 5S ribosomal RNA genes in evolutionary divergence anuran amphibians. Chromosoma 84:475–491PubMedCrossRefGoogle Scholar
  58. Ward RD, Holmes BH, O’Hara TD (2008) DNA barcoding discriminates echinoderm species. Mol Ecol Resour 8:1202–1211PubMedCrossRefGoogle Scholar
  59. Wares JP, Cunningham CW (2001) Phylogeography and historical ecology of the North Atlantic intertidal. Evolution 1:2455–2469Google Scholar
  60. Wasko AP, Cesar ACG, Martins C, Galetti PM (2001) A ZZ/ZW sex chromosome system in Cheirodontinae fish. Chromosome Sci 5:145–148Google Scholar
  61. Weitzman SH, Menezes NA, Weitzman MJ (1988) Phylogenetic biogeography of the glandulocaudini (Teleostei: Characiformes, Characidae) with comments on the distribution of other freshwater fishes in eastern and southeastern Brazil. In: Vanzolini PE, Heyer WR (eds) Proceedings of a workshop on neotropical distribution patterns. Academia Brasileira de Ciências, Rio de Janeiro, pp 379–427Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • T. C. Mariguela
    • 1
  • L. R. S. Paiva
    • 1
  • F. Foresti
    • 1
  • C. Oliveira
    • 1
  1. 1.Laboratório de Biologia e Genética de Peixes, Departamento de MorfologiaInstituto de Biociências de Botucatu, Universidade Estadual Paulista, UNESPBotucatuBrazil

Personalised recommendations