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Nat Genet. 2016 Jun;48(6):593-9. doi: 10.1038/ng.3559. Epub 2016 Apr 25.

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

Author information

1
Program in Biomedical Informatics, Stanford University, Stanford, California, USA.
2
Department of Genetics, Stanford University, Stanford, California, USA.
3
Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
4
Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
5
New York Genome Center, New York, New York, USA.
6
School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
7
Center for Evolution and Medicine, Biodesign Institute, Arizona State University, Tempe, Arizona, USA.
8
Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA.
9
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
10
Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, USA.
11
Institute for Molecular Bioscience, University of Queensland, St Lucia, Queensland, Australia.
12
Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
13
Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
14
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
15
Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, USA.
16
Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, Virginia, USA.
17
Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA.
18
Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
19
Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
20
Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea.
21
Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, New York, USA.
22
Center for Computational Biology and Bioinformatics, Columbia University, New York, New York, USA.
23
Department of Biomedical Data Science, Stanford University, Stanford, California, USA.

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.

Comment in

PMID:
27111036
PMCID:
PMC4884158
DOI:
10.1038/ng.3559
[Indexed for MEDLINE]
Free PMC Article

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