Phylogenetic relationships of Sakhalin taimen Parahucho perryi inferred from PCR-RFLP analysis of mitochondrial DNA

  • A. G. OleinikEmail author
  • L. A. Skurikhina
Experimental Articles


RFLP analysis of three amplified mtDNA fragments (Cytb/D-loop, ND1/ND2, and ND3/ND4L/ND4) was performed in the following taxa: Parahucho perryi, Hucho taimen, Brachymystax lenok, B. tumensis, Salmo salar, Salvelinus leucomaenis, and S. levanidovi. For mtDNA of P. perryi, a substantial decrease in the haplotype and nucleotide diversity was observed as a result of random genetic drift, caused by a reduction in the effective population size. Nucleotide divergence estimates between the mtDNA haplotypes were determined. Sakhalin taimen P. perryi was found to be approximately equally diverged from S. salar and from the charrs of the genus Salvelinus, by 11.0 and 10.0%, respectively. The divergence between P. perryi and H. taimen constituted 14.6%, between P. perryi and lenoks of the genus Brachymystax, 14.2%, and between H. taimen and Brachymystax, 7.7%. The analysis of possible phylogenetic relationships of the mtDNA from P. perryi among the group of taxa examined confirmed validity of the genus Parahucho. Phylogenetic reconstructions performed showed that robustness of the trees constructed for the complex of phylogenetically informative characters over three mtDNA fragments was considerably higher than that of the trees constructed for individual genes.


Parsimonious Tree RFLP Analysis Tree Length Elephant Seal Random Genetic Drift 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Viktorovsky, R.M., Makoedov, A.N., and Shevchishin, A.A., The Chromosome Sets of Brachymystax lenok and Siberian Hucho taimen and the Divergence of Salmonid Genera, Tsitologiya, 1985, vol. 27, no. 6, pp. 703–709.Google Scholar
  2. 2.
    Holcik, J., Hensel, K., Nieslanik, J., and Skacel, L., The Eurasian Huchen, Hucho hucho: Largest Salmon of the World, Dordrecht: Junk, 1988.Google Scholar
  3. 3.
    Dorofeeva, E.A., Basic Principles of Classification and Phylogeny of Salmonid Fishes (Salmoniformes, Salmonoidei, Salmonidae), in Biologiya i filogeniya ryb (Biology and Phylogeny of Fishes), Leningrad: Zool.Inst. AN SSSR, 1989, pp. 5–15.Google Scholar
  4. 4.
    Osinov, A.G., Genetic Divergence and Phylogenetic Relationships between Lenoks of Genus Brachymystax and Huchens of Genera Hucho and Parahucho, Genetika (Moscow), 1991, vol. 27, no. 12, pp. 2127–2136.Google Scholar
  5. 5.
    Stearley, R.Y. and Smith, G.R., Phylogeny of the Pacific Trout and Salmon (Oncorhynchus) and Genera of the Family Salmonidae, Trans. Am. Fish. Soc., 1993, vol. 122, no. 1, pp. 1–33.CrossRefGoogle Scholar
  6. 6.
    Glubokovsky, M.K., Evolyutsionnaya biologiya lososevykh ryb (Evolutionary Biology of Salmonid Fishes), Moscow: Nauka, 1995.Google Scholar
  7. 7.
    Oakley, T.H. and Phillips, R.B., Phylogeny of Salmonine Fishes Based on Growth Hormone Introns: Atlantic (Salmo) and Pacific (Oncorhynchus) Salmon Are Not Sister Taxa, Mol. Phylogenet. Evol., 1999, vol. 11, no. 3, pp. 381–393.PubMedCrossRefGoogle Scholar
  8. 8.
    Shedko S.V. Phylogeny of Mitochondrial DNA in Salmonids of the Subfamily Salmoninae: Analysis of the Cytochrome b Gene Sequences, Russ. J. Genet., 2002, vol. 38, no. 3, pp. 277–285.CrossRefGoogle Scholar
  9. 9.
    Vladykov, V.D. and Gruchy, C.D., Comments on the Nomenclature of Some Subgenera of Salmonidae, J. Fish. Res. Board Can., 1972, vol. 29, pp. 1631–1632.Google Scholar
  10. 10.
    Phillips, R.B., Oakley, T.H., and Davis, E.L., Evidence Supporting the Paraphyly of Hucho (Salmonidae) Based on Ribosomal DNA Restriction Maps, J. Fish. Biol., 1995, vol. 47, pp. 956–961.CrossRefGoogle Scholar
  11. 11.
    Phillips, R.B. and Oakley, T.H., Phylogenetic Relationships among the Salmoninae Based on Nuclear and Mitochondrial DNA Sequences, in Molecular Systematic of Fishes, San Diego: Academic, 1997, pp. 145–162.CrossRefGoogle Scholar
  12. 12.
    Oleinik, A.G. and Polyakova, N.E., Restriction Analysis of the Mitochondrial Genome in the Family Salmonidae, Russ. J. Genet., 1994, vol. 30, no. 9, pp. 1043–1050.Google Scholar
  13. 13.
    Shedko, S.V., Ginatulina, L.K., Parpura, I.Z., and Ermolenko, A.V., Evolutionary and Taxonomic Relationships among Far-Eastern Salmonids Fishes Inferred from Mitochondrial DNA Divergence, J. Fish Biol., 1996, vol. 49, pp. 815–829.CrossRefGoogle Scholar
  14. 14.
    Froufe, E., Alekseyev, S., Knizhin, I., and Weiss, S., Comparative mtDNA Sequence (Control Region, ATPase 6 and NADH1) Divergence in Hucho taimen (Pallas) across Four Siberian River Basins, J. Fish. Biol., 2005, vol. 67, no. 4, pp. 1040–1053.CrossRefGoogle Scholar
  15. 15.
    Crespi, B.J. and Fulton, M.J., Molecular Systematics of Salmonidae: Combined Nuclear Data Yields a Robust Phylogeny, Mol. Phylogenet. Evol., 2004, vol. 31, pp. 658–679.PubMedCrossRefGoogle Scholar
  16. 16.
    Oleinik, A.G. and Polyakova, N.E., Analiz mezhvidovoi geneticheskoi differentsiatsii u nekotorykh vidov sem. Salmonidae (Analysis of Interspecies Genetic Differentiation among Some Species of the Family Salmonidae), Available from VINITI, 1992, no. 1317-1392.Google Scholar
  17. 17.
    Froufe, E., Sefc, K.M., Alexandrino, P., and Weiss, S., Isolation and Characterization of Brachymystax lenok Microsatellite Loci and Cross-Species Amplification in Hucho spp. and Parahucho perryi, Mol. Ecol. Notes, 2004, vol. 4, no. 2, pp. 150–152.CrossRefGoogle Scholar
  18. 18.
    Bogutskaya, N.G. and Naseka, A.M., Katalog beschelyustnykh i ryb presnykh i solonovatykh vod Rossii s nomenklaturnymi i taksonomicheskimi kommentariyami (Catalog of Agnathous and Fish of the Fresh and Salt Waters of Russia), Moscow: Tovarishestvo nauchnych izd. KMK, 2004.Google Scholar
  19. 19.
    Sambrook, J., Fritsch, E.F., and Maniatis, T., Molecular Cloning: A Laboratory Manual, New York: Cold Spring Harbor Lab., 1989.Google Scholar
  20. 20.
    Gharrett, A.J., Gray, A.K., and Brykov, V.A., Mitochondrial DNA Variation in Alaskan Coho Salmon, Onchorhynchus kisutch, Fish. Bull., 2001, vol. 99, pp. 528–544.Google Scholar
  21. 21.
    Oleinik, A.G., Skurikhina, L.A., and Brykov, Vl.A., Divergence of the Salvelinus species mitochondrial DNA from northeastern Asia, Ecol. Freshwater Fish, 2007, vol. 16, no. 1, pp. 87–98.CrossRefGoogle Scholar
  22. 22.
    McElroy, D., Moran, P., Bermingham, E., and Kornfield, I., REAP: An Integrated Environment for the Manipulation and Phylogenetic Analysis of Restriction Data, J. Heredi. 1992, vol. 83, pp. 153–158.Google Scholar
  23. 23.
    Nei, M. and Li, W.-H., Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases, Proc. Natl Acad. Sci. USA, 1979, vol. 76, pp. 5269–5273.PubMedCrossRefGoogle Scholar
  24. 24.
    Nei, M. and Tajima, F., DNA Polymorphism Detectable by Restriction Endonucleases, Genetics, 1981, vol. 97, pp. 145–163.PubMedGoogle Scholar
  25. 25.
    Sneath, P.H.A. and Sokal, R.R., Numerical Taxonomy, San Francisco: Freeman, 1973.Google Scholar
  26. 26.
    Saitou, N. and Nei, M., The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees, Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.PubMedGoogle Scholar
  27. 27.
    Felsenstein, J., Confidence Limits on Phylogenies: An Approach Using Bootstrap, Evolution, 1985, vol. 39, pp. 783–791.CrossRefGoogle Scholar
  28. 28.
    Felsenstein, J., PHYLIP (Phylogeny Inference Package) Version 3.67, Washington, DC: Univ. Washington, 2007.Google Scholar
  29. 29.
    Swofford, D.L., PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods) Version 4.0b10, Sunderland: Sinauer, 2002.Google Scholar
  30. 30.
    Templeton, A.R., Phylogenetic Inference from Restriction Endonuclease Cleavage Site Maps with Particular Reference to the Evolution of Humans and the Apes, Evolution, 1983, vol. 37, pp. 221–244.CrossRefGoogle Scholar
  31. 31.
    Hendy, M.D. and Penny, D., Branch and Bound Algorithms to Determine Minimal Evolutionary Trees, Math. Biosci., 1982, vol. 59, pp. 277–290.CrossRefGoogle Scholar
  32. 32.
    Schneider, S., Roessli, D., and Excoffier, L., Arlequin, Version 2.000: A Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, Geneva: Univ. Geneva, 2000.Google Scholar
  33. 33.
    Tajima, F., Evolutionary Relationship of DNA Sequences in Finite Populations, Genetics, 1983, vol. 105, pp. 437–460.PubMedGoogle Scholar
  34. 34.
    Nei, M., Analysis of Gene Diversity in Subdivided Populations, Proc. Natl Acad. Sci. USA, 1973, vol. 70, pp. 3321–3323.PubMedCrossRefGoogle Scholar
  35. 35.
    Nei, M., Molecular Evolutionary Genetics, New York: Columbia Univ. Press, 1987.Google Scholar
  36. 36.
    Roff, D. and Bentzen, P., The Statistical Analysis of Mitochondrial DNA Polymorphisms: Chi-Square and the Problem of Small Samples, Mol. Biol. Evol., 1989, vol. 5, pp. 539–545.Google Scholar
  37. 37.
    Yamamoto, S., Morita, K., Kitano, S., et al., Phylogeography of White-Spotted Charr (Salvelinus leucomaenis) Inferred from Mitochondrial DNA Sequences, Zool. Sci., 2004, vol. 21, pp. 229–240.PubMedCrossRefGoogle Scholar
  38. 38.
    Altukhov, Yu.P., Geneticheskie protsessy v populyatsiyakh (Genetic Processes in Populations), Moscow: Akademkniga, 2003.Google Scholar
  39. 39.
    Brunner, P.C., Douglas, M.R., and Bernatchez, L., Microsatellite and Mitochondrial DNA Assessment of Population Structure and Stocking Effects in Arctic Charr Salvelinus alpines (Teleostei: Salmonidae) from Central Alpine Lakes, Mol. Ecol., 1998, vol. 7, pp. 209–223.CrossRefGoogle Scholar
  40. 40.
    Hartley, S.E., Bartlett, S.E., and Davidson, W.S., Mitochondrial DNA Analysis of Scottish Populations of Arctic Charr, Salvelinus alpines L., J. Fish Biol., 1992, vol. 40, pp. 219–224.CrossRefGoogle Scholar
  41. 41.
    Oleinik, A.G., Skurikhina, L.A., and Chukova, E.I., Effect of Isolation on the Genetics Characteristics of Populations in Chars of the Genus Salvelinus, Russ. J. Genet., 2007, vol. 43, no. 9, pp. 1006–1013.CrossRefGoogle Scholar
  42. 42.
    Allendorf, F.W., Christiansen, F.B., Dobson, T., et al., Electrophoretic Variation in Large Mammals: I. The Polar Bear, Thalarctos maritimus, Hereditas, 1979, vol. 91, pp. 19–22.PubMedCrossRefGoogle Scholar
  43. 43.
    Bonnell, M.L. and Selander, R.K., Elephant Seals: Genetic Variation and Near Extinction, Science, 1974, vol. 184, pp. 908–909.CrossRefGoogle Scholar
  44. 44.
    Kimura, M., The Neutral Theory of Molecular Evolution, Cambridge: Cambridge Univ., 1983.Google Scholar
  45. 45.
    Gritsenko, O.F. and Churikov, A.A., Issledovaniya ekologii taimenya Hucho perryi (Brevoort) Severnogo Sakhalina (Study of Taimen Hucho perryi (Brevoort) Ecology in Northern Sakhalin), Moscow: ONTI VNIRO, 1977.Google Scholar
  46. 46.
    Parpura, I.Z., Biology of Sakhalin Taimen Parahucho perryi and Chars of the Genus Salvelinus in Waters of Northern Primorye, Extended Abstract of Cand. Sci. (Biol.) Dissertation, Vladivostok: TINRO, 1991, p. 23.Google Scholar
  47. 47.
    Excoffier, L., Smouse, P.E., and Quattro, J.M., Analysis of Molecular Variance Inferred from Metric Distances among DNA Haplotypes: Application to Human Mitochondrial DNA Restriction Data, Genetics, 1992, vol. 131, pp. 479–491.PubMedGoogle Scholar
  48. 48.
    Churikov, D., M. Matsuoka, X. Luan Et Al. Assessment of Concordance among Genealogical Reconstruction’s from Various mtDNA Segments in Three Species of Pacific Salmon (Genus Oncorhynchus), Mol. Ecol., 2001, vol. 10, pp. 2329–2339.PubMedCrossRefGoogle Scholar
  49. 49.
    Cummings, M.P., Otto, S.P., and Wakeley, J., Sampling Properties of DNA Sequence Data in Phylogenetic Analysis, Mol. Biol. Evol., 1995, vol. 12, pp. 814–822.PubMedGoogle Scholar

Copyright information

© MAIK Nauka 2008

Authors and Affiliations

  1. 1.Zhirmunsky Institute of Marine BiologyRussian Academy of SciencesVladivostokRussia

Personalised recommendations