Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences.
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.
Program in Biomedical Informatics, Stanford University, Stanford, California, USA.|Department of Genetics, Stanford University, Stanford, California, USA.
G David
0000-0003-4427-3556
GD
Poznik
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Yali
Y
Xue
Department of Genetics, Stanford University, Stanford, California, USA.
Fernando L
FL
Mendez
Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.|New York Genome Center, New York, New York, USA.
Thomas F
TF
Willems
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Andrea
A
Massaia
School of Life Sciences, Arizona State University, Tempe, Arizona, USA.|Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
Melissa A
0000-0002-2614-0285
MA
Wilson Sayres
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Qasim
0000-0003-3291-0917
Q
Ayub
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Shane A
0000-0002-2715-4187
SA
McCarthy
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
Apurva
A
Narechania
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
Seva
S
Kashin
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Yuan
Y
Chen
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Ruby
R
Banerjee
Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA.
Juan L
JL
Rodriguez-Flores
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Maria
M
Cerezo
Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.
Haojing
H
Shao
New York Genome Center, New York, New York, USA.|Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
Melissa
M
Gymrek
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
Ankit
A
Malhotra
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Sandra
S
Louzada
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
Rob
R
Desalle
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Graham R S
GR
Ritchie
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
Eliza
E
Cerveira
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Tomas W
TW
Fitzgerald
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Erik
E
Garrison
Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.
Anthony
A
Marcketta
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA.|Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA.
David
D
Mittelman
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
Mallory
M
Romanovitch
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
Chengsheng
C
Zhang
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Xiangqun
X
Zheng-Bradley
Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
Gonçalo R
GR
Abecasis
Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Steven A
SA
McCarroll
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Paul
0000-0002-3897-7955
P
Flicek
Department of Genetics, Stanford University, Stanford, California, USA.
Peter A
PA
Underhill
Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.
Lachlan
L
Coin
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Daniel R
0000-0001-5350-3056
DR
Zerbino
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Fengtang
F
Yang
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.|Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea.
Charles
C
Lee
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
Laura
0000-0002-5989-6898
L
Clarke
Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.
Adam
A
Auton
New York Genome Center, New York, New York, USA.|Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA.|Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.
Yaniv
Y
Erlich
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.|Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
Robert E
0000-0002-3128-3547
RE
Handsaker
Department of Genetics, Stanford University, Stanford, California, USA.|Department of Biomedical Data Science, Stanford University, Stanford, California, USA.
Carlos D
CD
Bustamante
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
Chris
C
Tyler-Smith
D041322:Chromosomes, Human, Y; D003710:Demography; D006239:Haplotypes; D006801:Humans; D008297:Male; D009154:Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide