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

G. David Poznik; Yali Xue; Fernando L. Mendez; Thomas F. Willems; Andrea Massaia; Melissa A. Wilson Sayres; Qasim Ayub; Shane A. McCarthy; Apurva Narechania; Seva Kashin; Yuan Chen; Ruby Banerjee; Juan L. Rodriguez-Flores; Maria Cerezo; Haojing Shao; Melissa Gymrek; Ankit Malhotra; Sandra Louzada; Rob Desalle; Graham R.S. Ritchie; Eliza Cerveira; Tomas W. Fitzgerald; Erik Garrison; Anthony Marcketta; David Mittelman; Mallory Romanovitch; Chengsheng Zhang; Xiangqun Zheng-Bradley; Gon'alo R. Abecasis; Steven A. McCarroll; Paul Flicek; Peter A. Underhill; Lachlan Coin; Daniel R. Zerbino; Fengtang Yang; Charles Lee; Laura Clarke; Adam Auton; Yaniv Erlich; Robert E. Handsaker; Carlos D. Bustamante; Chris Tyler-Smith

doi:10.1038/ng.3559

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

G. David Poznik, Yali Xue, Fernando L. Mendez, Thomas F. Willems, Andrea Massaia, Melissa A. Wilson Sayres, Qasim Ayub, Shane A. McCarthy, Apurva Narechania, Seva Kashin, Yuan Chen, Ruby Banerjee, Juan L. Rodriguez-Flores, Maria Cerezo, Haojing Shao, Melissa Gymrek, Ankit Malhotra, Sandra Louzada, Rob Desalle, Graham R.S. RitchieEliza Cerveira, Tomas W. Fitzgerald, Erik Garrison, Anthony Marcketta, David Mittelman, Mallory Romanovitch, Chengsheng Zhang, Xiangqun Zheng-Bradley, Gon'alo R. Abecasis, Steven A. McCarroll, Paul Flicek, Peter A. Underhill, Lachlan Coin, Daniel R. Zerbino, Fengtang Yang, Charles Lee, Laura Clarke, Adam Auton, Yaniv Erlich, Robert E. Handsaker, Carlos D. Bustamante, Chris Tyler-Smith

Research output: Contribution to journal › Article › Research › peer-review

214 Citations (Scopus)

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.

Original language	English
Pages (from-to)	593-599
Number of pages	7
Journal	Nature Genetics
Volume	48
Issue number	6
DOIs	https://doi.org/10.1038/ng.3559
Publication status	Published - Jun 2016
Externally published	Yes

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Poznik, G. D., Xue, Y., Mendez, F. L., Willems, T. F., Massaia, A., Wilson Sayres, M. A., Ayub, Q., McCarthy, S. A., Narechania, A., Kashin, S., Chen, Y., Banerjee, R., Rodriguez-Flores, J. L., Cerezo, M., Shao, H., Gymrek, M., Malhotra, A., Louzada, S., Desalle, R., ... Tyler-Smith, C. (2016). Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences. Nature Genetics, 48(6), 593-599. https://doi.org/10.1038/ng.3559

@article{47b2fe3eeec548019316b8349534cc5a,

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

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.",

author = "Poznik, {G. David} and Yali Xue and Mendez, {Fernando L.} and Willems, {Thomas F.} and Andrea Massaia and {Wilson Sayres}, {Melissa A.} and Qasim Ayub and McCarthy, {Shane A.} and Apurva Narechania and Seva Kashin and Yuan Chen and Ruby Banerjee and Rodriguez-Flores, {Juan L.} and Maria Cerezo and Haojing Shao and Melissa Gymrek and Ankit Malhotra and Sandra Louzada and Rob Desalle and Ritchie, {Graham R.S.} and Eliza Cerveira and Fitzgerald, {Tomas W.} and Erik Garrison and Anthony Marcketta and David Mittelman and Mallory Romanovitch and Chengsheng Zhang and Xiangqun Zheng-Bradley and Abecasis, {Gon'alo R.} and McCarroll, {Steven A.} and Paul Flicek and Underhill, {Peter A.} and Lachlan Coin and Zerbino, {Daniel R.} and Fengtang Yang and Charles Lee and Laura Clarke and Adam Auton and Yaniv Erlich and Handsaker, {Robert E.} and Bustamante, {Carlos D.} and Chris Tyler-Smith",

year = "2016",

month = jun,

doi = "10.1038/ng.3559",

language = "English",

volume = "48",

pages = "593--599",

journal = "Nature Genetics",

issn = "1061-4036",

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Poznik, GD, Xue, Y, Mendez, FL, Willems, TF, Massaia, A, Wilson Sayres, MA, Ayub, Q, McCarthy, SA, Narechania, A, Kashin, S, Chen, Y, Banerjee, R, Rodriguez-Flores, JL, Cerezo, M, Shao, H, Gymrek, M, Malhotra, A, Louzada, S, Desalle, R, Ritchie, GRS, Cerveira, E, Fitzgerald, TW, Garrison, E, Marcketta, A, Mittelman, D, Romanovitch, M, Zhang, C, Zheng-Bradley, X, Abecasis, GR, McCarroll, SA, Flicek, P, Underhill, PA, Coin, L, Zerbino, DR, Yang, F, Lee, C, Clarke, L, Auton, A, Erlich, Y, Handsaker, RE, Bustamante, CD & Tyler-Smith, C 2016, 'Punctuated bursts in human male demography inferred from 1,244 worldwide Y-chromosome sequences', Nature Genetics, vol. 48, no. 6, pp. 593-599. https://doi.org/10.1038/ng.3559

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AU - Xue, Yali

AU - Mendez, Fernando L.

AU - Willems, Thomas F.

AU - Massaia, Andrea

AU - Wilson Sayres, Melissa A.

AU - Ayub, Qasim

AU - McCarthy, Shane A.

AU - Narechania, Apurva

AU - Kashin, Seva

AU - Chen, Yuan

AU - Banerjee, Ruby

AU - Rodriguez-Flores, Juan L.

AU - Cerezo, Maria

AU - Shao, Haojing

AU - Gymrek, Melissa

AU - Malhotra, Ankit

AU - Louzada, Sandra

AU - Desalle, Rob

AU - Ritchie, Graham R.S.

AU - Cerveira, Eliza

AU - Fitzgerald, Tomas W.

AU - Garrison, Erik

AU - Marcketta, Anthony

AU - Mittelman, David

AU - Romanovitch, Mallory

AU - Zhang, Chengsheng

AU - Zheng-Bradley, Xiangqun

AU - Abecasis, Gon'alo R.

AU - McCarroll, Steven A.

AU - Flicek, Paul

AU - Underhill, Peter A.

AU - Coin, Lachlan

AU - Zerbino, Daniel R.

AU - Yang, Fengtang

AU - Lee, Charles

AU - Clarke, Laura

AU - Auton, Adam

AU - Erlich, Yaniv

AU - Handsaker, Robert E.

AU - Bustamante, Carlos D.

AU - Tyler-Smith, Chris

PY - 2016/6

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AB - 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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U2 - 10.1038/ng.3559

DO - 10.1038/ng.3559

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SN - 1061-4036

VL - 48

SP - 593

EP - 599

JO - Nature Genetics

JF - Nature Genetics

IS - 6

ER -

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

Abstract

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