SpringerLink
Log in

Paleo-Siberian Substrate in the Gene Pool of Koryaks according to Data on Autosomal SNP Polymorphism and Y-Chromosome Haplogroups

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

Abstract—

The gene pool of the Koryaks was studied in comparison with other Far Eastern and Siberian peoples using a genome-wide panel of autosomal single-nucleotide polymorphic markers and Y-chromosome markers. The results of analyzing the frequencies of autosomal SNPs using various methods, the similarity in the composition of Y-chromosome haplogroups and YSTR haplotypes indicate that the gene pool of the Koryaks is as close as possible to the Chukchi one and was formed as a result of the unification of several groups whose ancestors had moved from the territory of modern Yakutia and the Amur region. The two dominant Y-chromosome haplogroups of the Koryaks with different sublines of haplotype clusters demonstrate their contacts with the Chukchi, Evens, Yukaghirs, and Eskimos. Analysis of the composition of genetic components and IBD blocks on autosomes indicates the maximum genetic proximity of the Koryaks to the Chukchi. Among the Siberian populations, the Chukchi, Koryaks, and Nivkhs form a cluster separate from the main group of Siberian populations, while the Chukchi and Koryaks are more closely related. Far Eastern populations are divided in full accordance with geographic localization into the northern group (Chukchi and Koryaks) and the southern group, including the Nivkhs and Udege. A more detailed analysis of the component composition of gene pools in some populations reveals components specific to them. The isolation of such components is associated with founder effects and a shift in allele frequencies for these populations. The Koryaks and Chukchi represent one of the most striking examples of long-standing genetic kinship. Their populations demonstrate maximum values of the level of genomic inbreeding FROH > 1.5 (0.0422, 0.0409), which is natural due to their relative isolation.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

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

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1.
Fig. 2.
Fig. 3.
Fig. 4.

Similar content being viewed by others

REFERENCES

  1. Results of the 2020 All-Russian Population Census. https://rosstat.gov.ru/vpn/2020.

  2. Pestryakov, A.P., Arctic race, in Bol’shaya rossiiskaya entsiklopediya (Great Russian Encyclopedia). https://old.bigenc.ru/ethnology/text/1828884.

  3. Balanovskaya, E.V., Bogunov, Yu.V., Bogunova, A.A., et al., Demographic portrait of the Koryaks from the northern Kamchatka, Vestn. Mosk. Univ., Ser. 23: Anthropol., 2020, no. 4, pp. 111—122. https://doi.org/10.32521/2074-8132.2020.4.111-122

  4. Levin, M.G., Etnicheskaya antropologiya i problemy etnogeneza narodov Dal’nego Vostoka (Ethnic Anthropology and Problems of Ethnogenesis of the Peoples of the Far East), Moscow: Akad. Nauk SSSR, 1958.

  5. Vdovin, I.S., Ocherki etnicheskoi istorii koryakov (Essays on the Ethnic History of Koryaks), Leningrad: Nauka, 1973.

  6. Vasil’evskii, R.S., Proiskhozhdenie i drevnyaya kul’tura koryakov (Origin and Ancient Culture of Koryaks), Novosibirsk: Nauka, 1971.

  7. Bat’yanova, E.P., Narody Severo-Vostoka Sibiri (Peoples of Northeast Siberia), Moscow: Nauka, 2010.

  8. Peoples of Russia, Bol’shaya rossiiskaya entsiklopediya (Great Russian Encyclopedia), Tishkov, V.A., Ed., Moscow: Bol'shaya Rossiiskaya Entsiklopediya, 1994.

  9. Grugni, V., Raveane, A., Ongaro, L., et al., Analysis of the human Y-chromosome haplogroup Q characterizes ancient population movements in Eurasia and the Americas, BMC Biol., 2019, no. 3. https://doi.org/10.1186/s12915-018-0622-4

  10. Liu, B.L., Ma, P.C., Wang, C.Z., et al., Paternal origin of Tungusic-speaking populations: insights from the updated phylogenetic tree of Y-chromosome haplogroup C2a-M86, Am. J. Hum. Biol., 2021, vol. 33, no. 2. https://doi.org/10.1002/ajhb.23462

  11. Derenko, M., Malyarchuk, B., Grzybowski, T., et al., Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in Northern Asia, PLoS One, 2010, vol. 5, no. 12. https://doi.org/10.1371/journal.pone.0015214

  12. Pagani, L., Lawson, D.J., Jagoda, E., et al., Genomic analyses inform on migration events during the peopling of Eurasia, Nature, 2016, no. 538, pp. 238—242. https://doi.org/10.1038/nature19792

  13. Rasmussen, M., Li, Y., Lindgreen, S., et al., Ancient human genome sequence of an extinct Palaeo-Eskimo, Nature, 2010, vol. 463, pp. 757—762. https://doi.org/10.1038/nature08835

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Karmin, M., Saag, L., Vicente, M., et al., A recent bottleneck of Y chromosome diversity coincides with a global change in culture, Genome Res., 2015, no. 25, pp. 459—466. https://doi.org/10.1101/gr.186684.114

  15. Malyarchuk, B., Derenko, M., Denisova, G., et al., Ancient links between Siberians and native Americans revealed by subty** the Y chromosome haplogroup Q1a, J. Hum. Genet., 2011, no. 56, pp. 583—588. https://doi.org/10.1038/jhg.2011.64

  16. Malyarchuk, B.A., Genetic markers on the distribution of ancient marine hunters in Priokhotye, Vavilovskii Zh. Genet. Sel., 2020, no. 24, no. 5, pp. 539—544. https://doi.org/10.18699/VJ20.646

  17. Dryomov, S.V., Nazhmidenova, A.M., Shalaurova, S.A., et al., Mitochondrial genome diversity at the Bering Strait area highlights prehistoric human migrations from Siberia to northern North America, Eur. J. Hum. Genet., 2015, no. 10, pp. 1399—1404. https://doi.org/10.1038/ejhg.2014.286

  18. Tamm, E., Kivisild, T., Reidla, M., et al., Beringian standstill and spread of Native American founders, PLoS One, 2007. https://doi.org/10.1371/journal.pone.0000829

  19. Guo, Y., He, J., Zhao, S., et al., Illumina human exome genoty** array clustering and quality control, Nat. Protoc., 2014, vol. 9, pp. 2643—2662.https://doi.org/10.1038/nprot.2014.174

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Ilumina GenomeStudio. https://emea.support.illumina.com/array/array_software/genomestudio/downloas.html.

  21. Browning, B.L. and Browning, S.R., Improving the accuracy and efficiency of identity-by-descent detection in population data, Genetics, 2013, vol. 194, no. 2, pp. 459—471. https://doi.org/10.1534/genetics.113.150029

    Article  PubMed  PubMed Central  Google Scholar 

  22. Browning, S.R. and Browning, B.L., Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering, Am. J. Hum. Genet., 2007, vol. 81, no. 5, pp. 1084—1097.https://doi.org/10.1086/521987

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Patterson, N., Price, A.L., and Reich, D., Population structure and eigenanalysis, PLoS Genet., 2006, vol. 2, no. 12, pp. 2074—2093. https://doi.org/10.1371/journal.pgen.0020190

    Article  CAS  Google Scholar 

  24. Menozzi, P., Piazza, A., and Cavalli-Sforza, L., Synthetic maps of human gene frequencies in Europeans, Science, 1978, vol. 201, no. 4358, pp. 786—792. https://doi.org/10.1126/science.356262

    Article  CAS  PubMed  Google Scholar 

  25. Skotte, L., Korneliussen, T., and Albrechtsen, A., Estimating individual admixture proportions from next generation sequencing data, Genetics, 2013, vol. 195, no. 3, pp. 693—702. https://doi.org/10.1534/genetics.113.154138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Alexander, D.H., Novembre, J., and Lange, K., Fast model-based estimation of ancestry in unrelated individuals, Genome Res., 2009, vol. 19, no. 9, pp. 1655—1664. https://doi.org/10.1101/gr.094052.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Alexander, D.H. and Lange, K., Enhancements to the ADMIXTURE algorithm for individual ancestry estimation, BMC Bioinf., 2011, vol. 12, pp. 212—246. https://doi.org/10.1186/1471-2105-12-246

    Article  Google Scholar 

  28. International Society of Genetic Genealogy. http://www.isogg.org/.

  29. Bandelt, H.J., Forster, P., and Röhl, A., Median-joining networks for inferring intraspecific phylogenies, Mol. Biol. Evol., 1999, vol. 16, pp. 37—48. https://doi.org/10.1093/oxfordjournals.molbev.a026036

    Article  CAS  PubMed  Google Scholar 

  30. Gol’tsova, T.V. and Osipova, L.P., Genetic and demographic structure of indigenous populatiions of Siberia in connection with problems of microevolution, Inf. Vestn. Vavilovskogo O-va. Genet. Sel., 2006, vol. 10, no. 1, pp. 126—154.

    Google Scholar 

  31. Evsyukov, A.N., Zhukova, O.V., and Rychkov, Yu.G., and Sheremetyeva, V.A., Gene geography of genetic processes in populations: gene migration in Siberia and the Russian Far East, Russ. J. Genet., 2000, vol. 36, no. 2, pp. 206—216.

    CAS  Google Scholar 

  32. Kolesnikov, N.A., Kharkov, V.N., Zarubin, A.A., et al., Features of the genomic distribution of runs of homozygosity in the indigenous population of northern Eurasia at the individual and population levels based on high density SNP analysis, Russ. J. Genet., 2021, vol. 57, no. 11, pp. 1271—1284. https://doi.org/10.1134/S1022795421110053

    Article  CAS  Google Scholar 

  33. Gusev, A., Kenny, E., Salit, J., et al., DASH: a method for identical-by-descent haplotype map** uncovers association with recent variation, Am. J. Human Genet., 2011, vol. 88, pp. 706—717. https://doi.org/10.1016/j.ajhg.2011.04.023

    Article  CAS  Google Scholar 

  34. Gurvich, I.S., Etnogenez narodov Severa (Ethnogenesis of the Peoples of the North), Moscow: Nauka, 1980.

  35. Damba, L.D., Gubina, M.A., Konchuk, Ch.D., et al., Representation of Mongoloid and Caucasoid mitochondrial DNA haplogroups in two indigenous populations of southern Siberia, in Genofond naseleniya Sibiri (Gene Pool of the Population of Siberia), Inst. Arkheol. Etnograf. Sib. Otd. Ross. Akad. Nauk, 2003, pp. 19—24.

  36. Voevoda, M.I., Avksentyuk, A.V., Ivanova, A.V., et al., Molecular genetic studies in the indigenous population of Chukotka: polymorphism analysis of mitochondrial DNA and the genes for alcohol-metabolizing enzymes, Sib. Ekol. Zh., 1994, vol. 1, no. 2, pp. 149—162.

    Google Scholar 

  37. Sukernik, R.I., Schurr, T.G., Starikovskaya, Y.B., and Wallace, D.C., Mitochondrial DNA variation in native Siberians with special reference to the evolutionary history of American Indians: I. Studies on restriction polymorphism, Russ. J. Genet., 1996, vol. 32, no. 3, pp. 376—382.

    CAS  Google Scholar 

  38. Starikovskaya, Y.B., Sukernik, R.I., Schurr, T.G., et al., mtDNA diversity in Chukchi and Siberian Eskimos: implications for the genetic history of Ancient Beringia and the peopling of the New World, Am. J. Hum. Genet. 1998, vol. 63, no. 5, pp. 1473—1491. https://doi.org/10.1086/302087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Derenko, M.V. and Malyarchuk, B.A., Genetic history of the indigenous population of Northern Asia, Priroda, 2002, vol. 10, pp. 69—76.

    Google Scholar 

  40. Bermisheva, M.A., Kutuev, I.A., Spitsyn, V.A., et al., Analysis of mitochondrial DNA variation in the population of Oroks, Russ. J. Genet., 2005, vol. 41, no. 1, pp. 66—71. https://doi.org/10.1007/PL00022112

    Article  CAS  Google Scholar 

Download references

Funding

This work was supported by the Russian Science Foundation, grant no. 22-64-00060, https://rscf.ru/project/22-64-00060/.

Author information

Authors and Affiliations

  1. Research Institute of Medical Genetics, Tomsk National Research Medical Center, Russian Academy of Sciences, 634050, Tomsk, Russia

    V. N. Kharkov, N. A. Kolesnikov, A. A. Zarubin, L. V. Valikhova, I. Yu. Khitrinskaya & V. A. Stepanov

  2. Federal Research Center of Fundamental and Translational Medicine, 630060, Novosibirsk, Russia

    M. I. Voevoda

  3. Ammosov North-Eastern Federal University, 677000, Yakutsk, Russia

    M. A. Gubina & A. L. Sukhomyasova

  4. Republican Hospital No. 1, National Medical Center, Yakutsk, Russia

    A. L. Sukhomyasova

Authors
  1. V. N. Kharkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. N. A. Kolesnikov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. A. A. Zarubin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. L. V. Valikhova
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. I. Yu. Khitrinskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. M. I. Voevoda
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. M. A. Gubina
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. A. L. Sukhomyasova
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. V. A. Stepanov
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. N. Kharkov.

Ethics declarations

ETHICS APPROVAL AND CONSENT TO PARTICIPATE

All studies were conducted in accordance with the principles of biomedical ethics as outlined in the 1964 Declaration of Helsinki and its later amendments. They were also approved by the Ethics Committee of the Research Institute of Medical Genetics of the Tomsk National Research Medical Center of the Russian Academy of Sciences (registration no. 223, protocol no. 15, dated February 28, 2023).

Informed consent was obtained from all individual participants involved in the study. All the examined are adults.

CONFLICT OF INTEREST

The authors of this work declare that they have no conflicts of interest.

Additional information

Publisher’s Note.

Pleiades Publishing remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Kharkov, V.N., Kolesnikov, N.A., Zarubin, A.A. et al. Paleo-Siberian Substrate in the Gene Pool of Koryaks according to Data on Autosomal SNP Polymorphism and Y-Chromosome Haplogroups. Russ J Genet 60, 787–796 (2024). https://doi.org/10.1134/S1022795424700236

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795424700236

Keywords:

Search

Navigation