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The Y-chromosome point mutation rate in humans

Helgason, Agnar, Einarsson, Axel W, Guðmundsdóttir, Valdís B, Sigurðsson, Ásgeir, Gunnarsdóttir, Ellen D, Jagadeesan, Anuradha, Ebenesersdóttir, S Sunna, Kong, Augustine, Stefánsson, Kári·2015·Nature Genetics

Abstract

Mutations are the fundamental source of biological variation, and their rate is a crucial parameter for evolutionary and medical studies. Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10(-10) mutations per position per year (PPPY). We observed a lower rate (P = 0.04) of 7.37 × 10(-10) PPPY for 6.1 Mb of sequence from palindromes (PAL), which was not statistically different from the rate of 7.2 × 10(-10) PPPY for paternally transmitted autosomes. We postulate that the difference between PAL and the other MSY regions may provide an indication of the rate at which nascent autosomal and PAL de novo mutations are repaired as a result of gene conversion.

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Crossref · 10.1038/ng.3171

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Citations

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Research works printed but not linked: 27

  1. Michaelson, J.J. et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell 151, 1431–1442 (2012). · DOI · Paper page
  2. Roach, J.C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010). · DOI · Paper page
  3. Sun, J.X. et al. A direct characterization of human mutation based on microsatellites. Nat. Genet. 44, 1161–1165 (2012). · DOI
  4. Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). · DOI
  5. 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). · DOI
  6. Rozen, S. et al. Abundant gene conversion between arms of palindromes in human and ape Y chromosomes. Nature 423, 873–876 (2003). · DOI
  7. Heyer, E., Puymirat, J., Dieltjes, P., Bakker, E. & de Knijff, P. Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. Hum. Mol. Genet. 6, 799–803 (1997). · DOI
  8. Xue, Y. et al. Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree. Curr. Biol. 19, 1453–1457 (2009). · DOI
  9. Poznik, G.D. et al. Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females. Science 341, 562–565 (2013). · DOI · Paper page
  10. Francalacci, P. et al. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science 341, 565–569 (2013). · DOI
  11. Scozzari, R. et al. An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa. Genome Res. 24, 535–544 (2014). · DOI
  12. Schrider, D.R., Hourmozdi, J.N. & Hahn, M.W. Pervasive multinucleotide mutational events in eukaryotes. Curr. Biol. 21, 1051–1054 (2011). · DOI
  13. Ballantyne, K.N. et al. Mutability of Y-chromosomal microsatellites: rates, characteristics, molecular bases, and forensic implications. Am. J. Hum. Genet. 87, 341–353 (2010). · DOI
  14. Cruciani, F. et al. A revised root for the human Y chromosomal phylogenetic tree: the origin of patrilineal diversity in Africa. Am. J. Hum. Genet. 88, 814–818 (2011). · DOI
  15. Elhaik, E., Tatarinova, T.V., Klyosov, A.A. & Graur, D. The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. Eur. J. Hum. Genet. 22, 1111–1116 (2014). · DOI
  16. Mendez, F.L. et al. An African American paternal lineage adds an extremely ancient root to the human Y chromosome phylogenetic tree. Am. J. Hum. Genet. 92, 454–459 (2013). · DOI
  17. Walsh, B. Estimating the time to the most recent common ancestor for the Y chromosome or mitochondrial DNA for a pair of individuals. Genetics 158, 897–912 (2001). · DOI
  18. Behar, D.M. et al. A “Copernican” reassessment of the human mitochondrial DNA tree from its root. Am. J. Hum. Genet. 90, 675–684 (2012). · DOI
  19. Ingman, M., Kaessmann, H., Paabo, S. & Gyllensten, U. Mitochondrial genome variation and the origin of modern humans. Nature 408, 708–713 (2000). · DOI
  20. McLaren, W. et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069–2070 (2010). · DOI
  21. Rosser, Z.H., Balaresque, P. & Jobling, M.A. Gene conversion between the X chromosome and the male-specific region of the Y chromosome at a translocation hotspot. Am. J. Hum. Genet. 85, 130–134 (2009). · DOI
  22. Trombetta, B., Cruciani, F., Underhill, P.A., Sellitto, D. & Scozzari, R. Footprints of X-to-Y gene conversion in recent human evolution. Mol. Biol. Evol. 27, 714–725 (2010). · DOI
  23. Trombetta, B., Sellitto, D., Scozzari, R. & Cruciani, F. Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes. Mol. Biol. Evol. 31, 2108–2123 (2014). · DOI
  24. Gudbjartsson, D.F. et al. Sequence variants from whole genome sequencing a large group of Icelanders. Sci. Data (in the press).
  25. Martin, E.R. et al. SeqEM: an adaptive genotype-calling approach for next-generation sequencing studies. Bioinformatics 26, 2803–2810 (2010). · DOI
  26. Harris, R.S. Improved Pairwise Alignment of Genomic DNA. PhD thesis. Penn. State Univ. (2007).
  27. Repping, S. et al. High mutation rates have driven extensive structural polymorphism among human Y chromosomes. Nat. Genet. 38, 463–467 (2006). · DOI

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Metadata

Authors
Helgason, A., Einarsson, A. W., Guðmundsdóttir, V. B., Sigurðsson, Á., Gunnarsdóttir, E. D., Jagadeesan, A., Ebenesersdóttir, S. S., Kong, A., & Stefánsson, K.
Venue
Nature Genetics
Published
2015-03-25
Volume
47
Issue
5
Pages
453-457
ISSN
  • 1061-4036
  • 1546-1718
Cited by
93
References
4
Language
en

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