Abstract
Y-chromosome short tandem repeats (STR) markers are widely used in human population genetic studies and forensic applications. Estimation of Y-STR mutation rate has a key role for dating the origin of Y chromosome lineages and for paternity tests. Previous studies demonstrated significant interlocus difference in mutation rate and the positive correlation to STR repeat length. The different ethnic groups and various Y-chromosome haplogroups defined by single-nucleotide polymorphisms were characterized by different Y-STR mutation rates. To date no Y-STR pedigree mutation studies were reported in native Siberian populations. Siberian Tundra Nentsi population possesses many unique genetic features and represents a good model for genealogical studies because of large family sizes, available ancestry information and relatively isolated life style in the extreme north environment. We thoroughly selected 50 paternal lineages with deep genealogical depth from 2 to 6 generations with the total number of 330 males. The number of descendants varied from 2 to 25 per paternal lineage, in average seven males per lineage. We also included in our analysis six Komi, three Russian and one Khant families who lived in the same villages. Totally 34 STR loci from non-recombining part of Y-chromosome were studied: DYS19, DYS390, DYS391, DYS393, DYS385A, DYS385B, DYS426, DYS388, DYS392, DYS439, DYS389-1, DYS389-2, DYS458, DYS447, DYS449, DYS459, DYS454, DYS464, DYS455, DYS457, DYS448, H4, DYS607, CDY-1, CDY-2, DYS460, YCA-1, YCA-2, DYS576, DYS570, DYS438, DYS456, DYS442, and C4. Eleven males (4%) had different alleles in six or seven STR loci compared to their paternal ancestors. We believe that those men were born out-of-wedlock or were adopted. Traditionally native Siberian people adopt and raise all children who lost their parents. Mutations were observed in 21 out of 34 Y-STR loci. We found relatively higher number of mutation gains (60%) versus losses. Our study has thus shown that the chosen Y-STR loci represent a powerful tool to estimate mutation rates for forensic and population genetic purposes.
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References
Underhill PA, Kivisild T (2007) Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet 41:539–564
Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P et al (2000) Y chromosome sequence variation and the history of human populations. Nat Genet 26:358–361
Hammer MF, Karafet TM, Redd AJ, Jarjanazi H, Santachiara-Benerecetti S, Soodyall H, Zegura SL (2001) Hierarchical patterns of global human Y-chromosome diversity. Mol Biol Evol 18:1189–1203
Karafet TM, Mendez FL, Meilerman MB, Underhill PA, Zegura SL, Hammer MF (2008) New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree. Genome Res 18(5):830–838
Kayser M, Kittler R, Erler A, Hedman M, Lee AC, Mohyuddin A, Mehdi SQ, Rosser Z, Stoneking M, Jobling MA et al (2004) A comprehensive survey of human Y-chromosomal microsatellites. Am J Hum Genet 74:1183–1197
Kayser M (2007) Uni-parental markers in human identity testing including forensic DNA analysis. Biotechniques 43:3042
de Knijff P (2000) Messages through bottlenecks: on the combined use of slow and fast evolving polymorphic markers on the human Y chromosome. Am J Hum Genet 67:1055–1061
Gusmao L, Alves C (2005) Y chromosome STR typing. Methods Mol Biol 297:67–82
White PS, Tatum OL, Deaven LL, Longmire JL (1999) New, male-specific microsatellite markers from the human Y chromosome. Genomics 57(3):433–437
Ayub Q, Mohyuddin A, Qamar R, Mazhar K, Zerjal T, Mehdi SQ, Tyler-Smith C (2000) Identification and characterisation of novel human Y-chromosomal microsatellites from sequence database information. Nucleic Acids Res 28(2):e8
Ballantyne KN, Goedbloed M, Fang R, Schaap O, Lao O, Wollstein A, Choi Y, van Duijn K, Vermeulen M, Brauer S, Decorte R, Poetsch M, von Wurmb-Schwark N, de Knijff P, Labuda D, Vézina H, Knoblauch H, Lessig R, Roewer L, Ploski R, Dobosz T, Henke L, Henke J, Furtado MR, Kayser M (2010) Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am J Hum Genet. doi:10.1016/j.ajhg.2010.08.006
Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo A, Jobling MA, de Knijff P, Kayser M, Krawczak M, Mayr WR, Morling N, Olaisen B, Pascali V, Prinz M, Roewer L, Schneider PM, Sajantila A, Tyler-Smith C (2001) DNA commission of the international society of forensic genetics: recommendations on forensic analysis using Y-chromosome STRs. Forensic Sci Int 124(1):5–10
Osipova LP, Posukh OL, Ivakin EA, Kryukov YuA, Karaphet TM (1996) Gene pool of native inhabitants of the Samburg Tundra Russ J Genet 32(6):722–728. Translated from Genetika (1996) 32(6):830–836
Duzhak TG, Osipova LP, Posukh OL, Chasovnikova OB, Ostashevskii VA, Lyakhovich VV (2001) Genetic polimorpisms of CYP1A1, GSTM1 and P53 genes in a unique Siberian population of Tundra Nentsi and its farmacogenetic importance. Int J Circumpolar Health 60:228–234
Karafet TM, Osipova LP, Gubina MA, Posukh OL, Zegura SL, Hammer MF (2002) High levels of Y-chromosome differentiation among native Siberian populations and the genetic signature of a boreal hunter-gatherer way of life. Hum Biol 74(6):761–789
Tambets K, Rootsi S, Kivisild T, Help H, Serk P, Loogvali EL, Tolk HV, Reidla M, Metspalu E, Pliss L, Balanovsky O, Pshenichnov A, Balanovska E, Gubina M, Zhadanov S, Osipova L et al (2004) The western and eastern roots of the Saami–the story of genetic “Outliers” told by mitochondrial DNA and Y chromosomes. Am J Hum Genet 74(4):661–682
Osipova LP, Posukh OL, Ponomareva AV, Matveeva V.G, Shcherbov BL, Strakhovenko VD, Sukhorukov FV (1999b) The Tundra Nentsy: health and environmental radiation on the territory they inhabit. In: Armannsson H (ed) The proceedings of the 5th international symposium on geochemistry of the earth’s surface, Reykjavik, 16–20 Aug 1999, pp 215–218
Osipova LP, Posukh OL, Koutzenogii KP, Sukhorukov FV, Matveeva VG, Grafodatskii AS, Konovalova NA, Sukhovey YG, Petrov SA, Lefranc G, Lefranc M-P (1999a). Epidemiological Studies for the Assessment of Risks from Environmental Radiation on Tundra Nentsi Population. In: Baumstark-Khan C et al (eds) NATO science series. Series 2: Environmental security. Proceedings of the NATO advanced research workshop “Fundamentals for the assessment of risks from environmental radiation”, vol 55, Brno, Czech republic, 6–10 Oct 1997, pp 35–42
Osipova LP, Koutsenogii KP, Shcherbov BL, Strakhovenko VD, Petrov SA (2002)Environmental radioactivity for risk assessment of health status in nature and human population of Northern Siberia. In:The 5-th international conference on environmental radioactivity in the Arctic and Antarctic, St. Petersburg, 16–20 June 2002, pp 124–127
Korovkina ES, Tuzikov FV, Tuzikova NA, Osipova LP, Buneva VN, Nevinsky GA (2004) The evaluation of biological health in the population of Tundra Nentsy (North-Western Siberia) from the data on autoantibodies and lipoproteins of the donors sera. Nucleosides Nucleotides Nucleic Acids 23(6/7):1009–1013
Redd AJ, Agellon AB, Kearney VA, Contreras VA, Karafet T, Park H, de Knijff P, Butler JM, Hammer MF (2002) Forensic value of 14 novel STRs on the human Y chromosome. Forensic Sci Int 130(2–3):97–111
Shen P, Wang F, Underhill PA, Franco C, Yang WH, Roxas A, Sung R, Lin AA, Hyman RW, Vollrath D et al (2000) Population genetic implications from sequence variation in four Y chromosome genes. Proc Natl Acad Sci 97:7354–7359
Tilford CA, Kuroda-Kawaguchi T, Skaletsky H, Rozen S, Brown LG, Rosenberg M, McPherson JD, Wylie K, Sekhon M, Kucaba TA, Waterston RH, Page DC (2001) A physical map of the human Y chromosome. Nature 409(6822):943–945
Underhill PA, Jin L, Lin AA, Mehdi SQ, Jenkins T, Vollrath D, Davis RW, Cavalli-Sforza LL, Oefner PJ (1997) Detection of numerous Y chromosome biallelic polymorphisms by denaturing high-performance liquid chromatography. Genome Res 7:996–1005
Y Chromosome, Consortium (2002) A nomenclature system for the tree of human Y-chromosomal binary haplogroups. Genome Res 12(2):339–348
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Osipova, L., Karafet, T., Hammer, M. (2012). De Novo Mutations in Y-Chromosome STR Loci Revealed in Paternal Lineages of Siberian Tundra Nentsi Population. In: Mothersill, C., Korogodina, V., Seymour, C. (eds) Radiobiology and Environmental Security. NATO Science for Peace and Security Series C: Environmental Security. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-1939-2_31
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DOI: https://doi.org/10.1007/978-94-007-1939-2_31
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