Abstract

We report the sequences of 1,244 human Y chromosomes randomly ascertained from 26 worldwide populations by the 1000 Genomes Project. We discovered more than 65,000 variants, including single-nucleotide variants, multiple-nucleotide variants, insertions and deletions, short tandem repeats, and copy number variants. Of these, copy number variants contribute the greatest predicted functional impact. We constructed a calibrated phylogenetic tree on the basis of binary single-nucleotide variants and projected the more complex variants onto it, estimating the number of mutations for each class. Our phylogeny shows bursts of extreme expansion in male numbers that have occurred independently among each of the five continental superpopulations examined, at times of known migrations and technological innovations.

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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.

Author information

Author notes

    • G David Poznik
    •  & Yali Xue

    These authors contributed equally to this work.

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

Consortia

  1. The 1000 Genomes Project Consortium

    A list of members and affiliations appears in the Supplementary Note.

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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.

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.

Corresponding authors

Correspondence to Carlos D Bustamante or Chris Tyler-Smith.

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–31, Supplementary Tables 1–19 and Supplementary Note.

Zip files

  1. 1.

    Supplementary Data

    Supplementary Data on SNVs, CNVs, STRs, haplogroups, phylogenetic analyses, functional annotations, mtDNA analysis, and expansion analyses.

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DOI

https://doi.org/10.1038/ng.3559

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