CoChat
Sign Up
Cited by 93

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

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
DOI 10.1038/ng.3171
Open this paper in CoChat — free account

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.

Overview

Integrity signals

Registry

Crossref · 10.1038/ng.3171

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Citations

Cites

Show all 4 references

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

Cited by

See all 93

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
Publisher
Springer Science and Business Media LLC
Published
2015-03-25
Volume
47
Issue
5
Pages
453-457
ISSN
  • 1061-4036
  • 1546-1718
DOI
10.1038/ng.3171
Cited by
93
References
4
Language
en
Licence
www.springer.com/tdm (tdm)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: The Y-chromosome point mutation rate in humans. https://app.cochat.ai/papers/10.1038/ng.3171
The paper
Helgason, A., Einarsson, A. W., Guðmundsdóttir, V. B., Sigurðsson, Á., Gunnarsdóttir, E. D., Jagadeesan, A., Ebenesersdóttir, S. S., Kong, A., & Stefánsson, K. (2015). The Y-chromosome point mutation rate in humans. Nature Genetics. https://doi.org/10.1038/ng.3171