Skip to main content
SpringerLink
Log in

Search for genetic markers of climatic adaptation in populations of North Eurasia

  • Reviews and Theoretical Articles
  • Published:
Russian Journal of Genetics Aims and scope Submit manuscript

Abstract

Genetic diversity of native populations of North Eurasia is investigated using a panel of genetic markers of candidate genes for cold climate adaptation. A high level of within- and between-population variability is detected. Comparative analysis of data on North Eurasian populations combined with data on worldwide populations from the 1000 Genomes and HDGP projects reveals correlations of genetic diversity in candidate genes for cold climate adaptation with key climate parameters, as well as the increase of genetic diversity in markers of this group of genes with the increase of latitude, that is, as modern humans migrated out of Africa. Using the method of searching for extreme empirical values of the coefficient of genetic diversity, signals of directional selection for markers of six genes adaptive to cold (MYOF, LONP2, IFNL4, MKL1, SLC2A12, and CPT1A) are found. The data are discussed in framework of the hypothesis of decanalization of genome–phenome relationships under the pressure of natural selection during human settlement throughout the world.

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. Malyarchuk, B.A., Derenko, M.V., Denisova, G.A., and Litvinov, A.N., Distribution of the arctic variant of the CPT1A gene in indigenous populations of Siberia, Vavilovskii Zh. Genet. Sel., 2016, vol. 20, no. 5, pp. 571–575. doi 10.18699/VJ16.130

    Google Scholar 

  2. Babenko, V.N., Isakova, Zh.T., Talaibekova, E.T., et al., Polymorphism in the TRP8 gene in Kyrgyz population: putative association with highland adaptation, Russ. J. Genet.: Appl. Res., 2016, vol. 6, no. 5, pp. 605–612. doi 10.1134/S2079059716050038

    Article  Google Scholar 

  3. Cardona, A., Pagani, L., Antao, T., et al., Genomewide analysis of cold adaptation in indigenous Siberian populations, PLoS One, 2014, vol. 9, no. 5, e98076. doi 10.1371/journal.pone.0098076

    Article  PubMed  PubMed Central  Google Scholar 

  4. Lappalainen, T., Salmela, E., Andersen, P.M., et al., Genomic landscape of positive natural selection in Northern European populations, Eur. J. Hum. Genet., 2010, vol. 18, pp. 471–478. doi 10.1038/ejhg.2009.184

    Article  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Hancock, A.M., Witonsky, D.B., Alkorta-Aranburu, G., et al., Adaptations to climate-mediated selective pressures in humans, PLoS Genet., 2011, vol. 7, no. 4, e1001375. doi 10.1371/journal.pgen.1001375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Stepanov, V.A., Etnogenomika naseleniya Severnoi Evrazii (Population Ethnogenomics of Northern Eurasia), Tomsk: Pechatnaya Manufaktura, 2002.

    Google Scholar 

  8. Khitrinskaya, I.Yu., Khar’kov, V.N., Voevoda, M.I, and Stepanov, V.A., Genetic diversity and relationships of populations of northern Eurasia by polymorphic Alu insertions, Mol. Biol. (Moscow), 2014, vol. 48, no. 1, pp. 58–68. doi 10.1134/S0026893314010051

    Article  CAS  Google Scholar 

  9. Cherednichenko, A.A., Trifonova, E.A., Vagaitseva, K.V., et al., Association of the genetic polymorphism of cytokines and their receptors with climate and geographic factors in human populations, Russ. J. Genet., 2014, vol. 50, no. 10, pp. 1112–1116. doi 10.1134/S1022795-414100020

    Article  CAS  Google Scholar 

  10. The 1000 Genomes Project Consortium, A global reference for human genetic variation, Nature, 2015, vol. 526, pp. 68–74. doi 10.1038/nature15393

    Article  PubMed Central  Google Scholar 

  11. Sudmant, P.H., Rausch, T., Gardner, E.J., et al., An integrated map of structural variation in 2504 human genomes, Nature, 2015, vol. 526, pp. 75–81. doi 10.1038/nature15394

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Cann, H.M., De Toma, C., Cazes, L., et al., A human genome diversity cell line panel, Science, 2002, vol. 296, no. 5566, pp. 261–262.

    Article  CAS  PubMed  Google Scholar 

  13. Stepanov, V.A., Vagajceva, K.V., Bocharova, A.V., and Khar’kov, V.N., Development of multiplex genotyping method of polymorphic markers for genes involved in human adaptation to cold climate, Sci. Evol., 2016, vol. 2, no. 2, pp. 92–101. doi 10.21603/2500–1418–2016–1–2–92–101

    Article  Google Scholar 

  14. Stepanov, V.A. and Trifonova, E.A., Multiplex SNP genotyping by MALDI-TOF mass spectrometry: frequencies of 56 immune response gene SNPs in human populations, Mol. Biol. (Moscow), 2013, vol. 47, no. 6, pp. 852–862. doi 10.1134/S0026893313060149

    Article  CAS  Google Scholar 

  15. Excoffier, L. and Lischer, H.E.L., Arlequin Suite ver. 3.5: a new series of programs to perform population genetics analyses under Linux and Windows, Mol. Ecol. Resour., 2010, vol. 10, pp. 564–567. doi 10.1111/j.1755- 0998.2010.02847.x

    Article  PubMed  Google Scholar 

  16. Stepanov, V.A., Khar’kov, V.N., Trifonova, E.A., and Marusin, A.V., Metody statisticheskogo analiza v populyatsionnoi i evolyutsionnoi genetike cheloveka: uchebnometodicheskoe posobie (Methods of Statistical Analysis in Population and Evolutionary Human Genetics: A Study Guide), in Ser. Nasledstvennost’ i zdorov’e, (Heredity and Health), Tomsk: Pechatnaya Manufaktura, 2014, issue 12.

    Google Scholar 

  17. Schlotterer, C., A microsatellite-based multilocus screen for the identification of local selective sweeps, Genetics, 2002, vol. 160, pp. 753–763.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Beaumont, M.A. and Balding, D.J., Identifying adaptive genetic divergence among populations from genome scans, Mol. Ecol., 2004, vol. 13, pp. 969–980.

    Article  CAS  PubMed  Google Scholar 

  19. Foll, M. and Gaggiotti, O.E., A genome scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective, Genetics, 2008, vol. 180, pp. 977–993. doi 10.1534/genetics.108.092221

    Article  PubMed  PubMed Central  Google Scholar 

  20. Excoffier, L., Hofer, T., and Foll, M., Detecting loci under selection in a hierarchically structured population, Heredity, 2009, vol. 103, pp. 285–298. doi 10.1038/hdy.2009.74

    Article  CAS  PubMed  Google Scholar 

  21. Stepanov, V.A., Kandelariya, P., Kkho, S., et al., Immune response decanalization in the resettlement of modern humans: the relationship of genetic diversity in the genes of the immune system with climatic and geographical factors, Med. Genet., 2013, no. 12, pp. 8–18.

    Google Scholar 

  22. Stepanov, V.A., Evolution of genetic diversity and human diseases, Russ. J. Genet., 2016, vol. 52, no. 7, pp. 746–756. doi 10.1134/S1022795416070103

    Article  CAS  Google Scholar 

  23. Pilewski, J.M., Latoche, J.D., Arcasoy, S.M., and Albelda, S.M., Expression of integrin cell adhesion receptors during human airway epithelial repair in vivo, Am. J. Physiol., 1997, vol. 273, pp. L256–L263.

    CAS  PubMed  Google Scholar 

  24. Demonbreun, A.R., Lapidos, K.A., Heretis, K., et al., Myoferlin regulation by NFAT in muscle injury, regeneration and repair, J. Cell Sci., 2010, vol. 123, pp. 2413–2422. doi 10.1242/jcs.065375

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Doherty, K.R., Cave, A., Davis, D.B., et al., Normal myoblast fusion requires myoferlin, Development, 2005, vol. 132, pp. 5565–5575. doi 10.1242/dev.02155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhang, Y. and Storey, K.B., Expression of nuclear factor of activated T cells (NFAT) and downstream muscle-specific proteins in ground squirrel skeletal and heart muscle during hibernation, Mol. Cell. Biochem., 2016, vol. 412, no. 27, pp. 27–40. doi 10.1007/s11010-015-2605-x

    Article  CAS  PubMed  Google Scholar 

  27. Venkatesh, S., Lee, J., Singh, K., et al., Multitasking in the mitochondrion by the ATP-dependent Lon protease, Biochim. Biophys. Acta, 2012, vol. 1823, no. 1, pp. 56–66. doi 10.1016/j.bbamcr.2011.11.003

    Article  CAS  PubMed  Google Scholar 

  28. Nordgren, M., Wang, B., Apanasets, O., and Fransen, M., Peroxisome degradation in mammals: mechanisms of action, recent advances, and perspectives, Front. Physiol., 2013, vol. 4, no. 145, pp. 92–103.

    Google Scholar 

  29. Elberg, G., Chen, L., Elberg, D., et al., MKL1 mediates TGF-beta1-induced alpha-smooth muscle actin expression in human renal epithelial cells, Am. J. Physiol. Renal Physiol., 2008, vol. 294, no. 5, pp. F1116–F1128. doi 10.1152/ajprenal.00142.2007

    Article  CAS  PubMed  Google Scholar 

  30. Amengual, J., Petrov, P., Bonet, M.L., et al., Induction of carnitine palmitoyl transferase 1 and fatty acid oxidation by retinoic acid in HepG2 cells, Int. J. Biochem. Cell Biol., 2012, vol. 44, no. 11, pp. 2019–2027. doi 10.1016/j.biocel.2012.07.026

    Article  CAS  PubMed  Google Scholar 

  31. Lemas, D.J., Wiener, H.W., O’Brien, D.M., et al., Genetic polymorphisms in carnitine palmitoyltransferase 1A gene are associated with variation in body composition and fasting lipid traits in Yup’ik Eskimos, J. Lipid Res., 2012, vol. 53, no. 1, pp. 175–184. doi 10.1194/jlr.P018952

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Biswas, S. and Akey, J.M., Genomic insights into positive selection, Trends Genet., 2006, vol. 22, no. 8, pp. 437–446. doi 10.1016/j.tig.2006.06.005

    Article  CAS  PubMed  Google Scholar 

  33. Sabeti, P.C., Varilly, P., Fry, B., et al., The International HapMap Consortium: genome-wide detection and characterization of positive selection in human populations, Nature, 2007, vol. 449, pp. 913–918. doi 10.1038/nature06250

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Izagirre, N. García, I., Junquera, C., et al., A scan for signatures of positive selection in candidate loci for skin pigmentation in humans, Mol. Biol. Evol., 2006, vol. 23, no. 9, pp. 1697–1706. doi 10.1093/molbev/msl030

    Article  CAS  PubMed  Google Scholar 

  35. Duforet-Frebourg, N., Luu, K., Laval, G., et al., Detecting genomic signatures of natural selection with principal component analysis: application to the 1000 genomes data, Mol. Biol. Evol., 2016, vol. 33, no. 4, pp. 1082–1093. doi 10.1093/molbev/msv33

    Article  CAS  PubMed  Google Scholar 

  36. Prokunina-Olsson, L., Muchmore, B., Tang, W., et al., A variant upstream of IFNL3 (IL28B) creating a new interferon gene IFNL4 is associated with impaired clearance of hepatitis C virus, Nat. Genet., 2013, vol. 45, pp. 164–171. doi 10.1038/ng.2521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Key, F.M., Peter, B., Dennis, M.Y., et al., Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of interferon lambda 4 (IFNL4), PLoS Genet., 2014, vol. 10, e1004681. doi 10.1371/journal.pgen.1004681

    Article  PubMed  PubMed Central  Google Scholar 

  38. Prokunina-Olsson, L., Tang, W., Gilyazova, I., et al., Population analysis of a frame-shift genetic variant that creates a novel interferon lambda 4 protein (ifnl4), in Genetics and Genomics of Global Health and Sustainability (Proc. Joint Conf. HGM 2013 and 21st International Congress of Genetics), 2013, p. 309.

    Google Scholar 

  39. Gibson, G., Decanalization and the origin of complex disease, Nat. Rev. Genet., 2009, vol. 10, no. 2, pp. 134–140. doi 10.1038/nrg2502

    Article  CAS  PubMed  Google Scholar 

  40. McGrath, J.J., Hannan, A.J., and Gibson, G., Decanalization, brain development and risk of schizophrenia, Transl. Psychiatry, 2011, vol. 1, e14. doi 10.1038/tp.2011.16

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

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

    V. A. Stepanov, V. N. Kharkov, K. V. Vagaitseva, A. V. Bocharova, A. A. Popovich & I. Yu. Khitrinskaya

  2. Department of Cytology and Genetics, National Research Tomsk State University, Tomsk, 634050, Russia

    V. A. Stepanov, V. N. Kharkov & K. V. Vagaitseva

  3. Tomsk Polytechnic University, Tomsk, 634050, Russia

    A. Yu. Kazantsev

Authors
  1. V. A. Stepanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. V. N. Kharkov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. K. V. Vagaitseva
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. A. V. Bocharova
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. A. Yu. Kazantsev
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. A. A. Popovich
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. I. Yu. Khitrinskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to V. A. Stepanov.

Additional information

Original Russian Text © V.A. Stepanov, V.N. Kharkov, K.V. Vagaitseva, A.V. Bocharova, A.Yu. Kazantsev, A.A. Popovich, I.Yu. Khitrinskaya, 2017, published in Genetika, 2017, Vol. 53, No. 11, pp. 1254–1266.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Stepanov, V.A., Kharkov, V.N., Vagaitseva, K.V. et al. Search for genetic markers of climatic adaptation in populations of North Eurasia. Russ J Genet 53, 1172–1183 (2017). https://doi.org/10.1134/S1022795417110114

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1022795417110114

Keywords

Search

Navigation