Global diversity, population stratification, and selection of human copy-number variation

Peter H. Sudmant; Swapan Mallick; Bradley J. Nelson; Fereydoun Hormozdiari; Niklas Krumm; John Huddleston; Bradley P. Coe; Carl Baker; Susanne Nordenfelt; Michael Bamshad; Lynn B. Jorde; Olga L. Posukh; Hovhannes Sahakyan; W. Scott Watkins; Levon Yepiskoposyan; M. Syafiq Abdullah; Claudio M. Bravi; Cristian Capelli; Tor Hervig; Joseph T.S. Wee; Chris Tyler-Smith; George Van Driem; Irene Gallego Romero; Aashish R. Jha; Sena Karachanak-Yankova; Draga Toncheva; David Comas; Brenna Henn; Toomas Kivisild; Andres Ruiz-Linares; Antti Sajantila; Ene Metspalu; Jüri Parik; Richard Villems; Elena B. Starikovskaya; George Ayodo; Cynthia M. Beall; Anna Di Rienzo; Michael F. Hammer; Rita Khusainova; Elza Khusnutdinova; William Klitz; Cheryl Winkler; Damian Labuda; Mait Metspalu; Sarah A. Tishkoff; Stanislav Dryomov; Rem Sukernik; Nick Patterson; David Reich; Evan E. Eichler

doi:10.1126/science.aab3761

Global diversity, population stratification, and selection of human copy-number variation

Peter H. Sudmant, Swapan Mallick, Bradley J. Nelson, Fereydoun Hormozdiari, Niklas Krumm, John Huddleston, Bradley P. Coe, Carl Baker, Susanne Nordenfelt, Michael Bamshad, Lynn B. Jorde, Olga L. Posukh, Hovhannes Sahakyan, W. Scott Watkins, Levon Yepiskoposyan, M. Syafiq Abdullah, Claudio M. Bravi, Cristian Capelli, Tor Hervig, Joseph T.S. WeeChris Tyler-Smith, George Van Driem, Irene Gallego Romero, Aashish R. Jha, Sena Karachanak-Yankova, Draga Toncheva, David Comas, Brenna Henn, Toomas Kivisild, Andres Ruiz-Linares, Antti Sajantila, Ene Metspalu, Jüri Parik, Richard Villems, Elena B. Starikovskaya, George Ayodo, Cynthia M. Beall, Anna Di Rienzo, Michael F. Hammer, Rita Khusainova, Elza Khusnutdinova, William Klitz, Cheryl Winkler, Damian Labuda, Mait Metspalu, Sarah A. Tishkoff, Stanislav Dryomov, Rem Sukernik, Nick Patterson, David Reich, Evan E. Eichler

Biology

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

Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Original language	English (US)
Article number	aab3761
Journal	Science
Volume	349
Issue number	6253
DOIs	https://doi.org/10.1126/science.aab3761
State	Published - Sep 11 2015

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Sudmant, P. H., Mallick, S., Nelson, B. J., Hormozdiari, F., Krumm, N., Huddleston, J., Coe, B. P., Baker, C., Nordenfelt, S., Bamshad, M., Jorde, L. B., Posukh, O. L., Sahakyan, H., Watkins, W. S., Yepiskoposyan, L., Abdullah, M. S., Bravi, C. M., Capelli, C., Hervig, T., ... Eichler, E. E. (2015). Global diversity, population stratification, and selection of human copy-number variation. Science, 349(6253), Article aab3761. https://doi.org/10.1126/science.aab3761

Sudmant, PH, Mallick, S, Nelson, BJ, Hormozdiari, F, Krumm, N, Huddleston, J, Coe, BP, Baker, C, Nordenfelt, S, Bamshad, M, Jorde, LB, Posukh, OL, Sahakyan, H, Watkins, WS, Yepiskoposyan, L, Abdullah, MS, Bravi, CM, Capelli, C, Hervig, T, Wee, JTS, Tyler-Smith, C, Van Driem, G, Romero, IG, Jha, AR, Karachanak-Yankova, S, Toncheva, D, Comas, D, Henn, B, Kivisild, T, Ruiz-Linares, A, Sajantila, A, Metspalu, E, Parik, J, Villems, R, Starikovskaya, EB, Ayodo, G, Beall, CM, Di Rienzo, A, Hammer, MF, Khusainova, R, Khusnutdinova, E, Klitz, W, Winkler, C, Labuda, D, Metspalu, M, Tishkoff, SA, Dryomov, S, Sukernik, R, Patterson, N, Reich, D & Eichler, EE 2015, 'Global diversity, population stratification, and selection of human copy-number variation', Science, vol. 349, no. 6253, aab3761. https://doi.org/10.1126/science.aab3761

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title = "Global diversity, population stratification, and selection of human copy-number variation",

abstract = "In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.",

author = "Sudmant, {Peter H.} and Swapan Mallick and Nelson, {Bradley J.} and Fereydoun Hormozdiari and Niklas Krumm and John Huddleston and Coe, {Bradley P.} and Carl Baker and Susanne Nordenfelt and Michael Bamshad and Jorde, {Lynn B.} and Posukh, {Olga L.} and Hovhannes Sahakyan and Watkins, {W. Scott} and Levon Yepiskoposyan and Abdullah, {M. Syafiq} and Bravi, {Claudio M.} and Cristian Capelli and Tor Hervig and Wee, {Joseph T.S.} and Chris Tyler-Smith and {Van Driem}, George and Romero, {Irene Gallego} and Jha, {Aashish R.} and Sena Karachanak-Yankova and Draga Toncheva and David Comas and Brenna Henn and Toomas Kivisild and Andres Ruiz-Linares and Antti Sajantila and Ene Metspalu and J{\"u}ri Parik and Richard Villems and Starikovskaya, {Elena B.} and George Ayodo and Beall, {Cynthia M.} and {Di Rienzo}, Anna and Hammer, {Michael F.} and Rita Khusainova and Elza Khusnutdinova and William Klitz and Cheryl Winkler and Damian Labuda and Mait Metspalu and Tishkoff, {Sarah A.} and Stanislav Dryomov and Rem Sukernik and Nick Patterson and David Reich and Eichler, {Evan E.}",

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doi = "10.1126/science.aab3761",

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T1 - Global diversity, population stratification, and selection of human copy-number variation

AU - Sudmant, Peter H.

AU - Mallick, Swapan

AU - Nelson, Bradley J.

AU - Hormozdiari, Fereydoun

AU - Krumm, Niklas

AU - Huddleston, John

AU - Coe, Bradley P.

AU - Baker, Carl

AU - Nordenfelt, Susanne

AU - Bamshad, Michael

AU - Jorde, Lynn B.

AU - Posukh, Olga L.

AU - Sahakyan, Hovhannes

AU - Watkins, W. Scott

AU - Yepiskoposyan, Levon

AU - Abdullah, M. Syafiq

AU - Bravi, Claudio M.

AU - Capelli, Cristian

AU - Hervig, Tor

AU - Wee, Joseph T.S.

AU - Tyler-Smith, Chris

AU - Van Driem, George

AU - Romero, Irene Gallego

AU - Jha, Aashish R.

AU - Karachanak-Yankova, Sena

AU - Toncheva, Draga

AU - Comas, David

AU - Henn, Brenna

AU - Kivisild, Toomas

AU - Ruiz-Linares, Andres

AU - Sajantila, Antti

AU - Metspalu, Ene

AU - Parik, Jüri

AU - Villems, Richard

AU - Starikovskaya, Elena B.

AU - Ayodo, George

AU - Beall, Cynthia M.

AU - Di Rienzo, Anna

AU - Hammer, Michael F.

AU - Khusainova, Rita

AU - Khusnutdinova, Elza

AU - Klitz, William

AU - Winkler, Cheryl

AU - Labuda, Damian

AU - Metspalu, Mait

AU - Tishkoff, Sarah A.

AU - Dryomov, Stanislav

AU - Sukernik, Rem

AU - Patterson, Nick

AU - Reich, David

AU - Eichler, Evan E.

PY - 2015/9/11

Y1 - 2015/9/11

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AB - In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

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SN - 0036-8075

VL - 349

JO - Science

JF - Science

IS - 6253

M1 - aab3761

ER -

Global diversity, population stratification, and selection of human copy-number variation

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