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The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks

  • Human Genetics
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Abstract

STR haplotypes of the Y chromosome are widely used as effective genetic markers in studies of human populations and in forensic DNA analysis. The task often arises to compare the spectrum of haplotypes in individuals or entire populations. Performing this task manually is too laborious and thus unrealistic. We propose an algorithm for counting similarity between STR haplotypes. This algorithm is suitable for massive analyses of samples. It is implemented in the computer program Haplomatch, which makes it possible to find haplotypes that differ from the target haplotype by 0, 1, 2, 3, or more mutational steps. The program may operate in two modes: comparison of individuals and comparison of populations. Flexibility of the program (the possibility of using any external database), its usability (MS Excel spreadsheets are used), and the capability of being applied to other chromosomes and other species could make this software a new useful tool in population genetics and forensic and genealogical studies. The Haplomatch software is freely available on our website www.genofond.ru. The program is applied to studying the gene pool of Cossacks. Experimental analysis of Y-chromosomal diversity in a representative set (N = 131) of Upper Don Cossacks is performed. Analysis of the STR haplotypes detects genetic proximity of Cossacks to East Slavic populations (in particular, to Southern and Central Russians, as well as to Ukrainians), which confirms the hypothesis of the origin of the Cossacks mainly due to immigration from Russia and Ukraine. Also, a small genetic influence of Turkicspeaking Nogais is found, probably caused by their occurrence in the Don Voisko as part of the Tatar layer. No similarities between haplotype spectra of Cossacks and Caucasus populations are found. This case study demonstrates the effectiveness of the Haplomatch software in analyzing large sets of STR haplotypes.

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References

  1. Gusmao, L., Sanchez-Diz, P., Calafell, F., et al., Mutation rates at Y chromosome specific microsatellites, Hum. Mutat., 2005, vol. 26, pp. 520–528. doi 10.1002/humu. 20254

    Article  CAS  PubMed  Google Scholar 

  2. Ge, J., Budowle, B., Aranda, X.G., et al., Mutation rates at Y chromosome short tandem repeats in Texas populations, Forensic Sci. Int. Genet., 2009, vol. 3, pp. 179–184. doi 10.1016/jfsigen.2009.01.007

    Article  CAS  PubMed  Google Scholar 

  3. Sanchez-Diz, P., Alves, C., Carvalho, E., et al., Population and segregation data on 17 Y-STRs: results of a GEP-ISFG collaborative study, Int. J. Legal. Med., 2008, vol. 122, pp. 529–533. doi 10.1007/s00414-0080265-z

    Article  PubMed  Google Scholar 

  4. Zhivotovsky, L.A., Underhill, P.A., Cinnioglu, C., et al., The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time, Am. J. Hum. Genet., 2004, vol. 74, pp. 50–61.

    CAS  PubMed  Google Scholar 

  5. Bandelt, H.J., Forster, P., Sykes, B.C., et al., Mitochondrial portraits of human populations using median networks, Genetics, 1995, vol. 141, pp. 743–753.

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Myres, N.M., Rootsi, S., Lin, A.A., et al., A major Ychromosome haplogroup R1b Holocene era founder effect in Central and Western Europe, Eur. J. Hum. Genet., 2011, vol. 19, no. 1, pp. 95–101. doi 10.1038/ejhg.2010

    Article  PubMed  PubMed Central  Google Scholar 

  7. Schneider, S., Roessli, D., and Excoffier, L., Arlequin, version 2.000 A Software for Population Genetics Data Analysis, Geneva: Univ. Geneva, 2000.

    Google Scholar 

  8. Balanovsky, O., Dibirova, K., Dybo, A., et al., Parallel evolution of genes and languages in the Caucasus region, Mol. Biol. Evol., 2011, vol. 28, no. 10, pp. 2905–2920. doi 10.1093/molbev/msr126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Zalloua, P.A., Xue, Y., Khalife, J., et al., Y-chromosomal diversity in Lebanon is structured by recent historical events, Am. J. Hum. Genet., 2008, vol. 82, pp. 873–882. doi 10.1016/jajhg.2008.01.020

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Zalloua, P.A., Platt, D.E., El ibai, M., et al., Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean, Am. J. Hum. Genet., 2008, vol. 83, pp. 633–642. doi 10.1016/jajhg.2008. 10.012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Willuweit, S. and Roewer, L., Y chromosome haplotype reference database (YHRD): update, Forensic Sci. Int. Genet., 2015, vol. 15, pp. 43–48. doi 10.1016/jfsigen.2014.11.024

    Article  CAS  PubMed  Google Scholar 

  12. Astapenko, M.P., Istoriya donskogo kazachestva v povestvovaniyakh i rasskazakh, v pyati tomakh (The History of the Don Cossacks in the Narratives and Stories in Five Volumes), Rostov-on-Don: Terra, 2000, vol. 1.

  13. Volkov, Yu.G., Donskie kazaki v proshlom i nastoyashchem (Don Cossacks in the Past and Present), Rostovon-Don GinGo, 1998.

    Google Scholar 

  14. Protsenko, B.N., Opposition “us-them” and the mentality of the Don Cossacks, in Istoriya i kul’tura narodov stepnogo Predkavkaz’ya i Severnogo Kavkaza: problemy mezhetnicheskikh otnoshenii (History and Culture of the Peoples of the Steppe Ciscaucasia and Northern Caucasus: Problems of Interethnic Relations), Rostov-onDon, 1999, pp. 211–221.

    Google Scholar 

  15. Roewer, L., Willuweit, S., Kruger, C., et al., Analysis of Y chromosome STR haplotypes in the European part of Russia reveals high diversities but non-significant genetic distances between populations, Int. J. Legal Med., 2008, vol. 122, no. 3, pp. 219–223. doi 10.1007/s00414-007-0222-2

    Article  PubMed  PubMed Central  Google Scholar 

  16. Slatkin, M., A measure of population subdivision based on microsatellite allele frequencies, Genetics, 1995, vol. 139, no. 1, pp. 457–462.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Nei, M., Molecular Evolutionary Genetics, New York Columbia Univ. Press, 1987.

    Google Scholar 

  18. Koshel’, S.M., Information technologies in genogeography, in Sovremennaya geograficheskaya kartografiya (Modern Geographic Cartography), Lur’e, I.K. and Kravtsova, V.I., Eds., Moscow: Data, 2012, pp. 158–166.

    Google Scholar 

  19. Pfeiffer, H., Brinkmann, B., Huhne, J., et al., Expanding the forensic German mitochondrial DNA control region database: genetic diversity as a function of sample size and microgeography, Int. J. Legal Med., 1999, vol. 112, no. 5, pp. 291–298.

    Article  CAS  PubMed  Google Scholar 

  20. Tetushkin, E.Ya., Genetic genealogy: history and methodology, Russ. J. Genet., 2011, vol. 47, no. 5, pp. 507–520.

    Article  CAS  Google Scholar 

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Authors and Affiliations

  1. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia

    M. I. Chukhryaeva, R. A. Skhalyakho, A. T. Agdzhoyan, Yu. V. Bogunov & O. P. Balanovsky

  2. Research Centre for Medical Genetics, Moscow, 115478, Russia

    M. I. Chukhryaeva, I. O. Ivanov, S. A. Frolova, R. A. Skhalyakho, A. T. Agdzhoyan, E. V. Balanovska & O. P. Balanovsky

  3. Department of Cartography and Geoinformatics, Moscow State University, Moscow, 119991, Russia

    S. M. Koshel

  4. Department of Genetics and Cytology, Kazarin Kharkiv National University, Kharkiv, 61022, Ukraine

    O. M. Utevska

Authors
  1. M. I. Chukhryaeva
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  2. I. O. Ivanov
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  3. S. A. Frolova
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  4. S. M. Koshel
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  5. O. M. Utevska
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  6. R. A. Skhalyakho
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  7. A. T. Agdzhoyan
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  8. Yu. V. Bogunov
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  9. E. V. Balanovska
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  10. O. P. Balanovsky
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Corresponding author

Correspondence to M. I. Chukhryaeva.

Additional information

Original Russian Text © M.I. Chukhryaeva, I.O. Ivanov, S.A. Frolova, S.M. Koshel, O.M. Utevska, R.A. Skhalyakho, A.T. Agdzhoyan, Yu.V. Bogunov, E.V. Balanovska, O.P. Balanovsky, 2016, published in Genetika, 2016, Vol. 52, No. 5, pp. 595–604.

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Chukhryaeva, M.I., Ivanov, I.O., Frolova, S.A. et al. The haplomatch program for comparing Y-chromosome STR-haplotypes and its application to the analysis of the origin of Don Cossacks. Russ J Genet 52, 521–529 (2016). https://doi.org/10.1134/S1022795416050045

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  • DOI: https://doi.org/10.1134/S1022795416050045

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