Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences (original) (raw)

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Acknowledgements

We thank the 1000 Genomes Project sample donors for making this work possible, all Project members for their contributions, and A. Martin for ADMIXTURE results. The tree in Figure 2 was drawn using FigTree. G.D.P. was supported by the National Science Foundation (NSF) Graduate Research Fellowship under grant DGE-1147470 and by National Library of Medicine training grant LM-007033. Work at the Wellcome Trust Sanger Institute (Q.A., R.B., M.C., Y.C., S.L., A. Massaia, S.A. McCarthy, C.T.-S., Y.X., and F.Y.) was supported by Wellcome Trust grant 098051. F.L.M. was supported by National Institutes of Health (NIH) grant 1R01GM090087, by NSF grant DMS-1201234, and by a postdoctoral fellowship from the Stanford Center for Computational, Evolutionary and Human Genomics (CEHG). T.F.W. was supported by an AWS Education Grant, and the work of T.F.W., M.G., and Y.E. was supported in part by NIJ award 2014-DN-BX-K089. M.C. is supported by a Fundación Barrié Fellowship. H.S. and L. Coin are supported by Australian Research Council grants DP140103164 and FT110100972, respectively. M.G. was supported by a National Defense Science and Engineering Graduate Fellowship. G.R.S.R. was supported by the European Molecular Biology Laboratory and the Sanger Institute through an EBI–Sanger Postdoctoral Fellowship. X.Z.-B., P.F., D.R.Z., and L. Clarke were supported by Wellcome Trust grants 085532, 095908, and 104947 and by the European Molecular Biology Laboratory. P.A.U. was supported by SAP grant SP0#115016. C.L. was supported in part by NIH grant U41HG007497. Y.E. holds a Career Award at the Scientific Interface from the Burroughs Wellcome Fund. C.D.B. was supported by NIH grant 5R01HG003229-09.

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Author notes

1. G David Poznik and Yali Xue: These authors contributed equally to this work.

Authors and Affiliations

1. Program in Biomedical Informatics, Stanford University, Stanford, California, USA
   G David Poznik
2. Department of Genetics, Stanford University, Stanford, California, USA
   G David Poznik, Fernando L Mendez, Peter A Underhill & Carlos D Bustamante
3. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK
   Yali Xue, Andrea Massaia, Qasim Ayub, Shane A McCarthy, Yuan Chen, Ruby Banerjee, Maria Cerezo, Sandra Louzada, Graham R S Ritchie, Tomas W Fitzgerald, Erik Garrison, Fengtang Yang & Chris Tyler-Smith
4. Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
   Thomas F Willems
5. New York Genome Center, New York, New York, USA
   Thomas F Willems, Melissa Gymrek & Yaniv Erlich
6. School of Life Sciences, Arizona State University, Tempe, Arizona, USA
   Melissa A Wilson Sayres
7. Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, USA
   Melissa A Wilson Sayres
8. Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
   Apurva Narechania & Rob Desalle
9. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
   Seva Kashin & Robert E Handsaker
10. Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA
    Juan L Rodriguez-Flores
11. Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia
    Haojing Shao & Lachlan Coin
12. Harvard–MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Melissa Gymrek
13. Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
    Ankit Malhotra, Eliza Cerveira, Mallory Romanovitch, Chengsheng Zhang & Charles Lee
14. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
    Graham R S Ritchie, Xiangqun Zheng-Bradley, Paul Flicek, Daniel R Zerbino & Laura Clarke
15. Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA
    Anthony Marcketta & Adam Auton
16. Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA.,
    David Mittelman
17. Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA.,
    David Mittelman
18. Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
    Gonçalo R Abecasis
19. Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Steven A McCarroll & Robert E Handsaker
20. Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
    Charles Lee
21. Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA
    Yaniv Erlich
22. Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA
    Yaniv Erlich
23. Department of Biomedical Data Science, Stanford University, Stanford, California, USA
    Carlos D Bustamante

Authors

1. G David Poznik
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2. Yali Xue
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3. Fernando L Mendez
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4. Thomas F Willems
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5. Andrea Massaia
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6. Melissa A Wilson Sayres
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7. Qasim Ayub
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8. Shane A McCarthy
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9. Apurva Narechania
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10. Seva Kashin
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11. Yuan Chen
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12. Ruby Banerjee
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13. Juan L Rodriguez-Flores
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14. Maria Cerezo
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15. Haojing Shao
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16. Melissa Gymrek
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17. Ankit Malhotra
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18. Sandra Louzada
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19. Rob Desalle
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20. Graham R S Ritchie
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21. Eliza Cerveira
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22. Tomas W Fitzgerald
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23. Erik Garrison
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24. Anthony Marcketta
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25. David Mittelman
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26. Mallory Romanovitch
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27. Chengsheng Zhang
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28. Xiangqun Zheng-Bradley
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29. Gonçalo R Abecasis
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30. Steven A McCarroll
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31. Paul Flicek
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32. Peter A Underhill
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33. Lachlan Coin
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34. Daniel R Zerbino
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35. Fengtang Yang
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36. Charles Lee
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37. Laura Clarke
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38. Adam Auton
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39. Yaniv Erlich
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40. Robert E Handsaker
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41. Carlos D Bustamante
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42. Chris Tyler-Smith
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The 1000 Genomes Project Consortium

Contributions

G.D.P., Y.X., C.D.B., and C.T.-S. conceived and designed the project. R.B., S.L., and F.Y. generated FISH data. A. Malhotra, M.R., E.C., C.Z., and C.L. generated aCGH data. G.D.P., Y.X., F.L.M., T.F.W., A. Massaia, M.A.W.S., Q.A., S.A. McCarthy, A.N., S.K., Y.C., J.L.R.-F., M.C., H.S., M.G., R.D., G.R.S.R., T.W.F., E.G., A. Marcketta, D.M., X.Z.-B., G.R.A., S.A. McCarroll, P.F., P.A.U., L. Coin, D.R.Z., L. Clarke, A.A., Y.E., R.E.H., C.D.B., and C.T.-S. analyzed the data. G.D.P., Y.X., F.L.M., T.F.W., A. Massaia, M.A.W.S., Q.A., and C.T.-S. wrote the manuscript. All authors reviewed, revised, and provided feedback on the manuscript.

Corresponding authors

Correspondence toCarlos D Bustamante or Chris Tyler-Smith.

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Competing interests

G.D.P. and A.A. are employees of 23andMe. P.F. is a member of the Scientific Advisory Board (SAB) for Omicia, Inc. P.A.U. has consulted for and owns stock options of 23andMe. Y.E. is an SAB member of Identify Genomics, BigDataBio, and Solve, Inc. C.D.B. is on the SABs of AncestryDNA, BigDataBio, Etalon DX, Liberty Biosecurity, and Personalis. He is also a founder and SAB chair of IdentifyGenomics. None of these entities had a role in the design, execution, interpretation, or presentation of this study.

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Poznik, G., Xue, Y., Mendez, F. et al. Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.Nat Genet 48, 593–599 (2016). https://doi.org/10.1038/ng.3559

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• Received: 08 November 2015
• Accepted: 01 April 2016
• Published: 25 April 2016
• Issue Date: June 2016
• DOI: https://doi.org/10.1038/ng.3559