Russian Journal of GeneticsRussian Journal of GeneticsГенетика0016-67583034-5103The Russian Academy of Sciences66695410.31857/S0016675824040099cqyburГЕНЕТИКА ЧЕЛОВЕКАResearch ArticleMutation rate estimates for Y chromosomal STRs in the Yakut populationОценка скорости возникновения мутаций в STR-локусах Y-хромосомы в якутской популяцииAdamovD. S.АдамовД. С.
Russian Federation
sardaanafedorova@mail.ruFedorovaS. A.ФедороваС. А.
Russian Federation
sardaanafedorova@mail.ruAmmosov North-Eastern Federal UniversityСеверо-Восточный федеральный университет им. М.К. Аммосова1104202460410411326022025Copyright ©; 2024, Russian Academy of SciencesCopyright ©; 2024, Российская академия наук2024Russian Academy of SciencesРоссийская академия наукhttps://transsyst.ru/0016-6758/article/view/666954

The fine structure of the Y chromosome haplogroup N3a2-M1982 has been described, based on complete sequencing data of 23 men, indigenous residents of Yakutia, taking into account both SNP and STR mutations. The rate of mutation of STR markers of the Y chromosome in the Yakut population was calibrated using radiocarbon dating of a sample of a medieval man, Yana Young, found in the lower reaches of the Yana River in Yakutia. Our estimates of the mutation intensity constant of STR loci in 23 marker haplotypes of the N3a2-M1991 branch using 3 different calculation options (0.0032, 0.0024, 0.0032) turned out to be slightly lower than the global average value according to YHRD data (0.0033), and higher than the average over frequently used for STR loci a “genealogical” mutation rate (0.0021), but within the confidence interval do not contradict modern ideas about STR mutations rate of the Y chromosome.

Впервые описана тонкая структура гаплогруппы N3a2-M1982 Y-хромосомы по данным полного секвенирования 23 мужчин, коренных жителей Якутии, с учетом как SNP-, так и STR-мутаций. Скорость мутирования STR-маркеров Y-хромосомы в якутской популяции была откалибрована по радиоуглеродной датировке образца средневекового мужчины Yana Young, найденного в нижнем течении р. Яна в Якутии. Полученные нами оценки константы интенсивности STR-мутаций в 23-маркерных гаплотипах ветви N3a2-M1991 с применением трех различных вариантов расчета (0.0032, 0.0024, 0.0032) оказались несколько ниже общемирового среднего значения по данным YHRD (0.0033), и выше усредненной “генеалогической” скорости мутирования (0.0021), но в пределах доверительного интервала не противоречат современным представлениям о скорости возникновения STR-мутаций в Y-хромосоме.

Y chromosomeSakha (Yakuts)STR locimutation rateY-хромосомасаха (якуты)STR-локусыскорость мутированияПравительство РФGovernment of the Russian FederationFSRG-2023-0003Fedorova S.A., Reidla M., Metspalu E. et al. Autosomal and uniparental portraits of the native populations of Sakha (Yakutia): Implications for the peopling of Northeast Eurasia // BMC Evol. Biology. 2013. V. 13. https://doi.org/10.1186/1471-2148-13-127Ilumäe A.M., Reidla M., Chukhryaeva M. et al. Human Y chromosome haplogroup N: A non-trivial time-resolved phylogeography that cuts across language families // Am. J. Hum. Genet. 2016, V. 99. P. 163–173. https://doi.org/10.1016/j.ajhg.2016.05.025Федорова С.А., Хуснутдинова Э.К. Особенности структуры генофонда и генетическая история саха (якутов) // Генетика. 2022. Т. 58. № 12. С. 1349–1366. https://doi.org/10.1134/S1022795422120031Адамов Д.С. Якутская ветвь игрек-хромосомы в составе гаплогруппы N-M2016 // Сибирские исследования. 2022. Т. 2. № 8. С. 6–14. http://doi.org/10.33384/26587270.2022.08.02.01rBergström A., McCarthy S., Hui R. et al. Insights into human genetic variation and population history from 929 diverse genomes // Science. 2020. V. 367(6484). https://doi.org/10.1126/science.aay5012Wong E., Khrunin A., Nichols L. et al. Reconstructing genetic history of Siberian and Northeastern European populations // Genome Res. 2015. V. 27. № 1. P. 1–14. https://doi.org/10.1101/gr.202945.115Karmin M., Saag L., Vicente M. et al. A recent bottleneck of Y chromosome diversity coincides with a global change in culture // Genome Res. 2015. V. 25. P. 459–466. https://doi.org/10.1101/gr.186684.114Sikora M., Pitulko V., Sousa V. et al. The population history of Northeastern Siberia since the Pleistocene // Nature. 2019. V. 570 (7760). P. 182–188. https://doi.org/10.1038/s41586-019-1279-zФедорова С.А., Попова С.А., Мордосова М.Л., Старостина М.И. Длина поколения в якутской популяции в XVIII–XIX вв. // Якутский мед. журнал. 2023. Т. 3 (83). С. 21–24. https://doi.org/10.25789/YMJ.2023.83.05Zvénigorosky V., Duchesne S., Romanova L. et al. The genetic legacy of legendary and historical Siberian chieftains // Communication Biology. 2020. V. 3(1). P. 581. https://doi.org/10.1038/s42003-020-01307-3Shi W., Ayub Q., Vermeulen M. et al. A worldwide survey of human male demographic history based on Y-SNP and Y-STR data from the HGDP-CEPH populations // Mol. Biol. Evol. 2010. V. 27. № 2. P. 385–393. https://doi.org/10.1093/molbev/msp243Gao T., Yun L., Gu Y. et al. Phylogenetic analysis and forensic characteristics of 12 populations using 23 Y-STR loci // Forensic Sci. Int. Genet. 2015. V. 19. P. 130–133. https://doi.org/10.1016/j.fsigen.2015.07.00613. Davis C., Ge J., Chidambaram A. et al. Y-STR loci diversity in native Alaskan populations // Int. J. Legal Med. 2011. V. 125. № 4. P. 559–563. https://doi.org/10.1007/s00414-011-0568-3Zvénigorosky V., Crubézy E., Gibert M. et al. The genetics of kinship in remote human groups // Forensic Sci. Int. Genet. 2016. V. 25. P. 52–62. https://doi.org/10.1016/j.fsigen.2016.07.018Балановский О.П., Запорожченко В.В. Хромосома-летописец: датировки генетики, события истории, соблазн ДНК-генеалогии January // Генетика. 2016. Т. 52. № 7. С. 810-830. https://doi.org/10.7868/S0016675816070043Gusmăo L., Sánchez-Diz P., Calafell F. et al. Mutation rates at Y chromosome specific microsatellites // Hum. Mutat. 2005. V. 26. № 6. P. 520–528. https://doi.org/10.1002/humu.20254Sánchez-Diz P., Alves C., Carvalho E. et al. Population and segregation data on 17 Y-STRs: Results of a GEPISFG collaborative study // Int. J. Legal Med. 2008. V. 122. № 6. P. 529–533. https://doi.org/10.1007/s00414-008-0265-zGe J., Budowle B., Aranda X.G. et al. Mutation rates at Y chromosome short tandem repeats in Texas populations // Forensic Sci. Int. Genet. 2009. V. 3. № 3. P. 179–184. https://doi.org/10.1016/j.fsigen.2009.01.007Burgarella С., Navasques M. Mutation rate estimates for 110 Y-chromosome STRs combining population and father-son pair data // Eur. J. Hum. Genet. 2011. V. 19 № 1. P. 70–75. https://doi.org/10.1038/ejhg.2010.154Zhivotovsky 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. № 1. P. 50–61. https://doi.org/10.1086/380911Willuweit S., Roewer L. The new Y Chromosome Haplotype Reference Database // Forensic Sci. Int. Genet. 2015. V. 15. P. 43–48. https://doi.org/10.1016/j.fsigen.2014.11.024Fu Q., Li H., Moorjani P. et al. Genome sequence of a 45000-year-old modern human from Western Siberia // Nature. 2014. V. 514. P. 445–449. https://doi.org/10.1038/nature13810Lee D.G., Kim S.J., Cho W.C. et al. Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs // Forensic Sci. Int. Genet. 2023. V. 65. https://doi.org/10.1016/j.fsigen.2023.102875Oh Y.N., Lee H.Y., Lee E.Y. et al. Haplotype and mutation analysis for newly suggested Y-STRs in Korean father-son pairs // Forensic Sci. Int. Genet. 2015. V. 15. P. 64–68. https://doi.org/10.1016/j.fsigen.2014.09.023Liu Z., Long G., Lang Y. et al. Sequence-based mutation patterns at 41 Y chromosomal STRs in 2 548 father-son pairs // Forensic Sci. Res. 2023. V. 8. № 2. P. 152–162. https://doi.org/10.1093/fsr/owad016Claerhout S., Vandenbosch M., Nivelle K. et al. Determining Y-STR mutation rates in deep-routing genealogies: Identification of haplogroup differences // Forensic Sci. Int. Genet. 2018. V. 34. P. 1–10. https://doi.org/10.1016/j.fsigen.2018.01.005Otagiri T., Sato N., Asamura H. et al. RMplex reveals population differences in RM Y-STR mutation rates and provides improved father-son differentiation in Japanese // Forensic Sci. Int. Genet. 2022. V. 61. https://doi.org/10.1016/j.fsigen.2022.102766Ralf A., Gonzalez D.M., Zandstra D. et al. Large-scale pedigree analysis highlights rapidly mutating Y-chromosomal short tandem repeats for differentiating patrilineal relatives and predicting their degrees of consanguinity // Hum. Genet. 2023. V. 142. № 1. P. 145–160. https://doi.org/10.1007/s00439-022-02493-2Willems T., Gymrek M., Poznik G.D. et al. Population-scale sequencing data enable precise estimates of Y-STR mutation rates // Am. J. Hum. Genet. 2016. V. 98. № 5. P. 919–933. https://doi.org/10.1016/j.ajhg.2016.04.001Ballantyne K.N., Keerl V., Wollstein A. et al. A new future of forensic Y-chromosome analysis: Rapidly mutating Y-STRs for differentiating male relatives and paternal lineages // Forensic Sci. Int. Genet. 2012. V. 6. № 2. P. 08–218. https://doi.org/10.1016/j.fsigen.2011.04.017