Skip to main content
SpringerLink
Log in

Genetic differentiation of sockeye salmon Oncorhynchus nerka from Kamchatka River basin and the lake–river systems of the west coast of the bering sea as inferred from data on single nucleotide polymorphism

  • Animal Genetics
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

The variability of 45 single nucleotide polymorphism loci (SNP) was studied in sockeye salmon from the Kamchatka River basin and four lake–river systems of the west coast of the Bering Sea. Based on the genetic differentiation estimates for the largest sockeye salmon populations of Eastern Kamchatka and Chukotka, the examined samples were combined into two regional groups represented by the population of the Kamchatka River drainage, which included numerous local subpopulations and seasonal races, and the northern population grouping from the rivers of Olutorsko–Navarinsky region, wherein the sockeye salmon from Maynypilginskaya Lake–River system was relatively isolated. Considerable divergence was observed between the island (Sarannoe Lake, Bering Island) and continental populations. Genetic heterogeneity was revealed and groups of earlyand late-maturing individuals were identified in the sample of late-run sockeye salmon from Kamchatka River. In Apuka River, subdivision of the spawning run into two genetically distinct spatial and temporal groupings was also observed. The results suggested that the differentiation of sockeye salmon samples by single nucleotide substitution frequencies was largely due to differences in the direction and strength of local selection at some loci in the population complexes and intrapopulation groupings from the examined river basins of Eastern Kamchatka, Chukotka, and Commander Islands.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Bugaev, V.F. and Kirichenko, V.E., Nagul’no-nerestovye ozera aziatskoi nerki (vklyuchaya nekotorye drugie vodoemy areala) (Rearing and Spawning Lakes for Asian Sockeye Salmon Stocks (Including Several Additional Water Bodies in Range)), Petropavlovsk-Kamchatskii: Kamchatpress, 2008.

    Google Scholar 

  2. Bugaev, V.F., Nerka reki Kamchatki (biologiya, chislennost’, promysel) (Sockeye Salmon of the Kamchatka River), Petropavlovsk-Kamchatskii: Kamchatpress, 2010.

    Google Scholar 

  3. Altukhov, Yu.P., Geneticheskie protsessy v populyatsiyakh (Genetic Processes in Populations), Moscow: Akademkniga, 2003, 3rd ed.

    Google Scholar 

  4. Novosel’skaya, A.Yu., Novosel’skii, Yu.I., and Altukhov, Yu.P., Physico-chemical characteristics and genetic heterogeneity of the sockeye salmon Oncorhynchus nerka (Walbaum) spawning herd from Lake Azabache, Genetika (Moscow), 1982, vol. 18, no. 6, pp. 1004–1011.

  5. Varnavskaya, N.V., Geneticheskaya differentsiatsiya populyatsii tikhookeanskikh lososei (Genetic Differentiation among Populations of Pacific Salmon), Petropavlovsk-Kamchatskii: Kamchatskii Nauchno-Issled. Inst. Rybn. Khoz. Okeanogr., 2006.

    Google Scholar 

  6. Pustovoit, S.P., Genetic heterogeneity of the sockeye salmon Oncorhynchus nerka (Walb.) spawning herd from the Kamchatka River, Genetika (Moscow), 1993, vol. 29, no. 5, pp. 808–819.

    Google Scholar 

  7. Shpigal’skaya, N.Yu., Shaporev, R.A., Zboeva, E.N., and Varnavskaya, N.V., Genetic differentiation at allozyme loci among local populations of sockeye salmon, Oncorhynchus nerka (Walbaum), in the Kamchatka River basin (Kamchatka Peninsula), in Populyatsionnaya biologiya, genetika i sistematika gidrobiontov (Population Biology, Genetics, and Systematics of Hydrobionts), Petropavlovsk-Kamchatskii, 2005, vol. 1, pp. 97–113.

    Google Scholar 

  8. Varnavskaya, N.V., Wood, C.C., and Everett, R., Genetic variation in sockeye salmon (Oncorhynchus nerka) populations of Asia and North America, Can. J. Fish. Aquat. Sci., 1994, vol. 51, suppl. 1, pp. 132–146.

    Article  Google Scholar 

  9. Brykov, Vl.A., Polyakova, N.E., Podlesnykh, A.V., et al., The effect of reproduction biotopes on the genetic differentiation of populations of sockeye salmon Oncorhynchus nerka, Russ. J. Genet., 2005, vol. 41, no. 5, pp. 509–517.

    Article  CAS  Google Scholar 

  10. Beacham, T.D., Varnavskaya, N.V., McIntosh, B., and MacConnachie, C., Population structure of sockeye salmon (Oncorhynchus nerka) from Russia determined with microsatellite DNA variation, Trans. Am. Fish. Soc., 2006, pp. 97–109.

    Google Scholar 

  11. Pil’ganchuk, O.A. and Shpigal’skaya, N.Yu., Genetic differentiation of sockeye salmon Oncorhynchus nerka (Walbaum, 1792) populations of eastern Kamchatka, Russ. J. Mar. Biol., 2013, vol. 39, no. 5, pp. 373–380.

    Article  Google Scholar 

  12. Khrustaleva, A.M., Volkov, A.A., Stoklitskaia, D.S., et al., Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka, Russ. J. Genet., 2010, vol. 46, no. 11, pp. 1362–1372.

    Article  CAS  Google Scholar 

  13. Pustovoit, S.P., Intrapopulational genetic variation and interpopulational differentiation of Asian Sockeye Salmon Oncorhynchus nerka (Walbaum), Russ. J. Genet., 1994, vol. 30, no. 1, pp. 101–106.

    Google Scholar 

  14. Gorbachev, V.V., A new limitation of microsatellite markers for their use in population research by the example of panmictic populations, Vavilov. Zh. Genet. Sel., 2011, vol. 15, no. 4, pp. 746–749.

    Google Scholar 

  15. Khrustaleva, A.M., Variability of size-age indices and genetic variability of sockeye salmon Oncorhynchus nerka from the Western Coast of Kamchatka: comparative analysis of methods of differentiation of local populations, J. Ichthyol., 2010, vol. 50, no. 5, pp. 362–373.

    Article  Google Scholar 

  16. Altukhov, Yu.P. and Salmenkova, E.A., DNA polymorphism in population genetics, Russ. J. Genet., 2002, vol. 38, no. 9, pp. 989–1008.

    Article  CAS  Google Scholar 

  17. Bugaev, V.F., Aziatskaya nerka (presnovodnyi period zhizni, struktura lokal’nykh stad, dinamika chislennosti) (Asian Sockeye Salmon (Freshwater Period of Life, Local Stock Structure, and Population Number Dynamics)), Moscow: Kolos, 1995.

    Google Scholar 

  18. Maniatis, T., Fritsch, E.F., and Sambrook, J., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor: Cold Spring Harbor Lab., 1982.

    Google Scholar 

  19. Habicht, C., Seeb, L.W., Myers, K.W., et al., Summer–fall distribution of stocks of immature sockeye salmon in the Bering Sea as revealed by single-nucleotide polymorphisms, Trans. Am. Fish. Soc., 2010, vol. 139, no. 4, pp. 1171–1191.

    Article  CAS  Google Scholar 

  20. Smith, C.T., Elfstrom, C.M., Seeb, J.E., and Seeb, L.W., Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon, Mol. Ecol., 2005, vol. 14, pp. 4193–4203.

    Article  CAS  PubMed  Google Scholar 

  21. Elfstrom, C.M., Smith, C.T., and Seeb, J.E., Thirtytwo single nucleotide polymorphism markers for highthroughput genotyping of sockeye salmon, Mol. Ecol. Notes, 2006, vol. 6, no. 4, pp. 1255–1259.

    Article  CAS  Google Scholar 

  22. Seeb, J.E., Pascal, C.E., Ramakrishnan, R., and Seeb, L.W., SNP genotyping by the 5'-nuclease reaction: advances in high throughput genotyping with non-model organisms, in Methods in Molecular Biology, Single Nucleotide Polymorphisms, Komar, A., Ed., New York: Humana, 2009, 2nd ed., pp. 277–292.

    Chapter  Google Scholar 

  23. Khrustaleva, A.M., Gritsenko, O.F., and Klovach, N.V., Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula, Russ. J. Genet., 2013, vol. 49, no. 11, pp. 1155–1167.

    Article  CAS  Google Scholar 

  24. Khrustaleva, A.M., Klovach, N.V., Gritsenko, O.F., and Sib, D.E., Intraand interpopulation variability of southwestern Kamchatka sockeye salmon Oncorhynchus nerka inferred from the data on single nucleotide polymorphism, Russ. J. Genet., 2014, vol. 50, no. 7, pp. 736–748.

    Article  CAS  Google Scholar 

  25. Pritchard, J.K., Stephens, M., and Donnelly, P., Inference of population structure using multilocus genotype data, Genetics, 2000, vol. 155, no. 2, pp. 945–959.

    PubMed Central  CAS  PubMed  Google Scholar 

  26. Gomez-Uchida, D., Seeb, J.E., Smith, M.J., et al., Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon populations, BMC Evol. Biol., 2011, vol. 11, p. 48. http://www.biomedcentral.com/14712148/11/48

    Article  PubMed Central  PubMed  Google Scholar 

  27. Pil’ganchuk, O.A., Genetic structure of sockeye salmon, Oncorhynchus nerka (Walbaum), of Kamchatka Peninsula, Cand. Sci. (Biol.) Dissertation, Petropavlovsk-Kamchatskii: Kamchatka Res. Inst. Fish. Oceanogr., 2014.

    Google Scholar 

  28. Altukhov, Yu.P., Salmenkova, E.A., and Omelchenko, V.T., Populyatsionnaya genetika lososevykh ryb (Population Genetics of Salmonid Fish), Moscow: Nauka, 1997.

    Google Scholar 

  29. Krogius, F.V., Seasonal races of red Oncorhynchus nerka (Walb.) and its spawning grounds in the water bodies of Kamchatka, in Biologicheskie osnovy razvitiya lososevogo khozyaistva v vodoemakh SSSR (The Biological Basis of Salmon Husbandry in Water Bodies of the USSR), Moscow: Nauka, 1983, pp. 18–31.

    Google Scholar 

  30. Il’ina, L.V., Dinamika chislennosti i geneticheskogo sostava populyatsii nerki ozera Azabach’ego (Population dynamics and genetic structure of populations of sockeye salmon in Lake Azabache), Available from VINITI, 1987.

    Google Scholar 

  31. Klovach, N.V. and Roi, V.I., Structure of the school of sock-eyed salmon Oncorhynchus nerka from the Apuka River (the Northeastern Kamchatka), J. Ichtyol., 2010, vol. 50, no. 4, pp. 460–464.

    Article  Google Scholar 

  32. Berg, L.S., Ryby presnykh vod SSSR i sopredel’nykh stran (Freshwater Fishes of the Soviet Union and Adjacent Countries), Moscow: Akad. Nauk SSSR, 1948, part 1, 4th ed.

    Google Scholar 

  33. Ivankov, V.N., Ecotops of salmonid fishes, in Morfologiya i sistematika lososevykh ryb (Morphology and Systematics of Salmonid Fishes), Leningrad: Zool. Inst. Akad. Nauk SSSR, 1985, pp. 47–54.

    Google Scholar 

  34. Konovalov, S.M., Populyatsionnaya biologiya tikhookeanskikh lososei (Population Biology of Pacific Salmons), Moscow: Nauka, 1980.

    Google Scholar 

  35. Glubokovskii, M.K., Evolyutsionnaya biologiya lososevykh ryb (Evolutionary Biology of Salmonid Fishes), Moscow: Nauka, 1995.

    Google Scholar 

  36. Gordeeva, N.V., High estimates of differentiation between pink salmon, Oncorhynchus gorbuscha, populations at locus of major histocompatibility complex MHC-I A1 support the “local stock” hypothesis, J. Ichtyol., 2012, vol. 52, no. 1, pp. 68–76.

    Article  Google Scholar 

  37. Amineva, V.A. and Yarzhombek, A.A., Fiziologiya ryb (Fish Physiology), Moscow: Legkaya i Pishchevaya Promyshlennost’, 1984.

    Google Scholar 

  38. Nikol’skii, G.V., Ekologiya ryb (Fish Ecology), Moscow: Vysshaya Shkola, 1974.

    Google Scholar 

  39. Ackerman, M.W., Habicht, C., and Seeb, L.W., Singlenucleotide polymorphisms (SNPs) under diversifying selection provide increased accuracy and precision in mixed-stock analyses of sockeye salmon from the Copper River, Alaska, Trans. Am. Fish. Soc., 2011, vol. 140, no. 3, pp. 865–881.

    Article  Google Scholar 

  40. Creelman, E.K., Hauser, L., Simmons, R.K., et al., Temporal and geographic genetic divergence: characterizing sockeye salmon populations in the Chignik watershed, Alaska, using single-nucleotide polymorphisms, Trans. Am. Fish. Soc., 2011, vol. 140, no. 3, pp. 749–762.

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Russian Federal Research Institute of Fisheries and Oceanography, Moscow, 107140, Russia

    A. M. Khrustaleva, N. V. Klovach & E. V. Vedischeva

  2. School of Aquatic and Fishery Sciences, University of Washington, 355020, Seattle, USA

    J. E. Seeb

Authors
  1. A. M. Khrustaleva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. V. Klovach
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. E. V. Vedischeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. J. E. Seeb
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to A. M. Khrustaleva or J. E. Seeb.

Additional information

Original Russian Text © A.M. Khrustaleva, N.V. Klovach, E.V. Vedischeva, J.E. Seeb, 2015, published in Genetika, 2015, Vol. 51, No. 10, pp. 1141–1153.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Khrustaleva, A.M., Klovach, N.V., Vedischeva, E.V. et al. Genetic differentiation of sockeye salmon Oncorhynchus nerka from Kamchatka River basin and the lake–river systems of the west coast of the bering sea as inferred from data on single nucleotide polymorphism. Russ J Genet 51, 980–991 (2015). https://doi.org/10.1134/S1022795415090057

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795415090057

Keywords

Search

Navigation