Abstract
Y chromosome microsatellite (Y-STR) diversity has been studied in different Mongolic-speaking populations from South Siberia, Mongolia, North-East China and East Europe. The results obtained indicate that the Mongolic-speaking populations clustered into two groups, with one group including populations from eastern part of South Siberia and Central Asia (the Buryats, Barghuts and Khamnigans) and the other group including populations from western part of Central Asia and East Europe (the Mongols and Kalmyks). High frequency of haplogroup C3-M407 (>50%) is present in the Buryats, Barghuts and Khamnigans, whereas in the Mongols and Kalmyks its frequency is much lower. In addition, two allelic combinations in DYS385a,b loci of C3-M407 haplotypes have been observed: the combination 11,18 (as well as 11,17 and 11,19) is frequent in different Mongolic-speaking populations, but the 11,11 branch is present mainly in the Kalmyks and Mongols. Results of locus-specific sequencing suggest that the action of gene conversion is a more likely explanation for origen of homoallelic 11,11 combination. Moreover, analysis of median networks of Y-STR haplotypes demonstrates that at least two gene conversion events can be revealed—one of them has probably occurred among the Mongols, and the other event occurred in the Barghuts. These two events give an average gene conversion rate range of 0.24–7.1 × 10–3 per generation.
Similar content being viewed by others
Login or create a free account to read this content
Gain free access to this article, as well as selected content from this journal and more on nature.com
or
References
Yunusbayev, B., Metspalu, M., Metspalu, E., Valeev, A., Litvinov, S., Valiev, R. et al. The genetic legacy of the expansion of Turkic-speaking nomads across Eurasia. PLoS Genet. 11, e1005068 (2015).
Malyarchuk, B., Derenko, M., Denisova, G., Khoit, S., Wozniak, M., Grzybowski, T. et al. Y-chromosome diversity in the Kalmyks at the ethnical and tribal levels. J. Hum. Genet. 58, 804–811 (2013).
Kharkov, V. N., Khamina, K. V., Medvedeva, O. F., Simonova, K. V., Eremina, E. R. & Stepanov, V. A. Gene pool of Buryats: clinal variability and territorial subdivision based on data of Y chromosome markers. Russ. J. Genet. 50, 180–190 (2014).
Derenko, M., Malyarchuk, B., Denisova, G., Perkova, M., Rogalla, U., Grzybowski, T. et al. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS ONE 7, e32179 (2012).
Derenko, M., Malyarchuk, B., Grzybowski, T., Denisova, G., Dambueva, I., Perkova, M. et al. Phylogeographic analysis of mitochondrial DNA in northern Asian populations. Am. J. Hum. Genet. 81, 1025–1041 (2007).
Malyarchuk, B., Derenko, M., Denisova, G., Woźniak, M., Grzybowski, T., Dambueva, I. et al. Phylogeography of the Y-chromosome haplogroup C in northern Eurasia. Ann. Hum. Genet. 74, 539–546 (2010).
Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P. J., Cordum, H. S., Hillier, L., Brown, L. G. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003).
Rozen, S., Skaletsky, H., Marszalek, J. D., Minx, P. J., Cordum, H. S., Waterston, R. H. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873–876 (2003).
Hallast, P., Balaresque, P., Bowden, G. R., Ballereau, S. & Jobling, M. A. Recombination dynamics of a human Y-chromosomal palindrome: Rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions. PLoS Genet. 9, e1003666 (2013).
Balaresque, P., King, T. E., Parkin, E. J., Heyer, E., Carvalho-Silva, D., Kraaijenbrink, T. et al. Gene conversion violates the stepwise mutation model for microsatellites in Y-chromosomal palindromic repeats. Hum. Mutat. 35, 609–617 (2014).
Karafet, T. M., Mendez, F. L., Meilerman, M. B., Underhill, P. A., Zegura, S. L. & Hammer, M. F. New binary polymorphisms reshape and increase resolution of the human Y-chromosomal haplogroup tree. Genome Res. 18, 830–838 (2008).
Karmin, M., Saag, L., Vicente, M., Wilson Sayres, M. A., Järve, M., Talas, U. G. et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture. Genome Res. 25, 459–466 (2015).
Woźniak, M., Derenko, M., Malyarchuk, B., Dambueva, I., Grzybowski, T. & Miścicka-Śliwka, D. Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia. Forensic Sci. Int. 164, 271–275 (2006).
Rogalla, U., Woźniak, M., Swobodziński, J., Derenko, M., Malyarchuk, B. A., Dambueva, I. et al. A novel multiplex assay amplifying 13 Y-STRs characterized by rapid and moderate mutation rate. Forensic Sci. Int. Genet. 15, 49–55 (2015).
Kittler, R., Erler, A., Brauer, S., Stoneking, M. & Kayser, M. Apparent intrachromosomal exchange on the human Y chromosome explained by population history. Eur. J. Hum. Genet. 11, 304–314 (2003).
Park, M. J., Shin, K.-J., Kim, N. Y., Yang, W. I., Cho, S.-H. & Lee, H. Y. Characterization of deletions in the DYS385 flanking region and null alleles associated with AZFc microdeletions in Koreans. J. Forensic Sci. 53, 331–334 (2008).
Dulik, M. C., Osipova, L. P. & Schurr, T. G. Y-chromosome variation in Altaian Kazakhs reveals a common paternal gene pool for Kazakhs and the influence of Mongolian expansions. PLoS ONE 6, e17548 (2011).
He, J. & Guo, F. Population genetics of 17 Y-STR loci in Chinese Manchu population from Liaoning Province, Northeast China. Forensic Sci. Int. Genet. 7, e84–e85 (2013).
Zhu, B., Wu, Y., Shen, C., Yang, T., Deng, Y., Xun, X. et al. Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China. Forensic Sci. Int. 175, 238–243 (2008).
Derenko, M., Malyarchuk, B., Denisova, G. A., Woźniak, M., Dambueva, I., Dorzhu, C. et al. Contrasting patterns of Y-chromosome variation in South Siberian populations from Baikal and Altai-Sayan regions. Hum. Genet. 118, 591–604 (2006).
Derenko, M., Malyarchuk, B., Denisova, G. A., Woźniak, M., Grzybowski, T., Dambueva, I. et al. Y-chromosome haplogroup N dispersals from south Siberia to Europe. J. Hum. Genet. 52, 763–770 (2007).
Malyarchuk, B., Derenko, M., Denisova, G., Maksimov, A., Woźniak, M., Grzybowski, T. et al. Ancient links between Siberians and Native Americans revealed by subtyping the Y chromosome haplogroup Q1a. J. Hum. Genet. 56, 583–588 (2011).
Excoffier, L. & Lischer, H. E. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Resour. 10, 564–567 (2010).
Slatkin, M. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 457–462 (1995).
Willuweit, S. & Roewer, L. The new Y chromosome haplotype reference database. Forensic Sci. Int. Genet. 15, 43–48 (2015).
Zhivotovsky, L. A., Underhill, P. A., Cinnioglu, C., Kayser, M., Morar, B., Kivisild, T. et al. The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am. J. Hum. Genet. 74, 50–61 (2004).
Ballantyne, K. N., Goedbloed, M., Fang, R., Schaap, O., Lao, O., Wollstein, A. et al. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am. J. Hum. Genet. 87, 341–353 (2010).
Matsumura, S. & Forster, P. Generation time and effective population size in Polar Eskimos. Proc. Biol. Sci. 275, 1501–1508 (2008).
Goedbloed, M., Vermeulen, M., Fang, R. N., Lembring, M., Wollstein, A., Ballantyne, K. et al. Comprehensive mutation analysis of 17 Y-chromosomal short tandem repeat polymorphisms included in the AmpFlSTR Yfiler PCR amplification kit. Int. J. Legal Med. 123, 471–482 (2009).
Hallast, P., Batini, C., Zadik, D., Maisano Delser, P., Wetton, J. H., Arroyo-Pardo, E. et al. The Y-chromosome tree bursts into leaf: 13,000 high-confidence SNPs covering the majority of known clades. Mol. Biol. Evol. 32, 661–673 (2015).
Bandelt, H.-J., Macaulay, V. & Richards, M. Median networks: speedy construction and greedy reduction, one simulation, and two case studies from human mtDNA. Mol. Phylogenet. Evol. 16, 8–28 (2000).
Wierdl, M., Dominska, M. & Petes, T. D. Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 146, 768–779 (1997).
Kayser, M., Kittler, R., Erler, A., Hedman, M., Lee, A. C., Mohyuddin, A. et al. A comprehensive survey of human Y-chromosomal microsatellites. Am. J. Hum. Genet. 74, 1183–1197 (2004).
Pugach, I., Matveev, R., Spitsyn, V., Makarov, S., Novgorodov, I., Osakovsky, V. et al. The complex admixture history and recent southern origens of Siberian populations. bioRxiv http://dx.doi.org/10.1101/018770 (2015).
Shubin, A. C. Brief Essay of Ethnic History of the Evenks from Trans-Baikal Region (XVIII-XX centries) (Buryat Publishing House, Ulan-Ude, Russia, 1973).
Buraev, I. D. & Shagdarov, L. D. in The Buryats (eds Abaeva, L. L. & Zhukovskaja, N. L.) 227–250 (Nauka, Moscow, Russia, 2004).
Dashibalov, B. B. Archaeological Sites of Kurykan and Khori (Buryat Scientific Center of SBRAS, Ulan-Ude, Russia, 1995).
Acknowledgements
This research was financially supported by the Program of Presidium of Russian Academy of Sciences ‘Basic research for the development of the Russian Arctic’.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no conflict of interest.
Additional information
Supplementary Information accompanies the paper on Journal of Human Genetics website
Supplementary information
Rights and permissions
About this article
Cite this article
Malyarchuk, B., Derenko, M., Denisova, G. et al. Y chromosome haplotype diversity in Mongolic-speaking populations and gene conversion at the duplicated STR DYS385a,b in haplogroup C3-M407. J Hum Genet 61, 491–496 (2016). https://doi.org/10.1038/jhg.2016.14
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/jhg.2016.14
This article is cited by
-
Mitogenomics of modern Mongolic-speaking populations
Molecular Genetics and Genomics (2022)
-
Phylogenetic analysis of the Y-chromosome haplogroup C2b-F1067, a dominant paternal lineage in Eastern Eurasia
Journal of Human Genetics (2020)
-
Mitogenomic diversity and differentiation of the Buryats
Journal of Human Genetics (2018)
-
Whole sequence analysis indicates a recent southern origen of Mongolian Y-chromosome C2c1a1a1-M407
Molecular Genetics and Genomics (2018)
