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

GD Poznik; Y Xue; FL Mendez; TF Willems; A Massaia; MA Wilson Sayres; Q Ayub; SA McCarthy; A Narechania; S Kashin; Y Chen; R Banerjee; JL Rodriguez-Flores; M Cerezo; H Shao; M Gymrek; A Malhotra; S Louzada; R Desalle; GRS Ritchie; E Cerveira; TW Fitzgerald; E Garrison; A Marcketta; D Mittelman; M Romanovitch; C Zhang; X Zheng-Bradley; GR Abecasis; SA McCarroll; P Flicek; PA Underhill; L Coin; DR Zerbino; F Yang; C Lee; L Clarke; A Auton; Y Erlich; RE Handsaker; CD Bustamante; C Tyler-Smith

Journal article

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

GD Poznik, Y Xue, FL Mendez, TF Willems, A Massaia, MA Wilson Sayres, Q Ayub, SA McCarthy, A Narechania, S Kashin, Y Chen, R Banerjee, JL Rodriguez-Flores, M Cerezo, H Shao, M Gymrek, A Malhotra, S Louzada, R Desalle, GRS Ritchie Show all

Nature Genetics | NATURE PORTFOLIO | Published : 2016

DOI: 10.1038/ng.3559

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 e..

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University of Melbourne Researchers

Lachlan Coin Author

Grants

Awarded by National Defense Science and Engineering Graduate

Funding 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 Fundacion Barrie 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.