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

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

doi:10.1126/science.aab3761

Author(s)

Sudmant, Peter H

Mallick, Swapan

Jorde, Lynn B

Posukh, Olga L

Sahakyan, Hovhannes

Watkins, W Scott

Yepiskoposyan, Levon

Abdullah, M Syafiq

Bravi, Claudio M

Capelli, Cristian

Hervig, Tor

Wee, Joseph T S

Nelson, Bradley J

Tyler-Smith, Chris

van Driem, George

Romero, Irene Gallego

Jha, Aashish R

Karachanak-Yankova, Sena

Toncheva, Draga

Comas, David

Henn, Brenna

Kivisild, Toomas

Ruiz-Linares, Andres

Hormozdiari, Fereydoun

Sajantila, Antti

Metspalu, Ene

Parik, Juri

Villems, Richard

Starikovskaya, Elena B

Ayodo, George

Beall, Cynthia M

Di Rienzo, Anna

Hammer, Michael F

Khusainova, Rita

Krumm, Niklas

Khusnutdinova, Elza

Klitz, William

Winkler, Cheryl

Labuda, Damian

Metspalu, Mait

Tishkoff, Sarah A

Dryomov, Stanislav

Sukernik, Rem

Patterson, Nick

Reich, David

Huddleston, John

Eichler, Evan E

Coe, Bradley P

Baker, Carl

Nordenfelt, Susanne

Bamshad, Michael

Publication Date

2015

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.

Citation

Science, 349(6253), p. 1-9

ISSN

1095-9203

0036-8075

Link

https://hdl.handle.net/1959.11/20607

Language

en

Publisher

American Association for the Advancement of Science (AAAS)

Title

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

Type of document

Journal Article

Entity Type

Publication

Author(s)	Sudmant, Peter H Mallick, Swapan Jorde, Lynn B Posukh, Olga L Sahakyan, Hovhannes Watkins, W Scott Yepiskoposyan, Levon Abdullah, M Syafiq Bravi, Claudio M Capelli, Cristian Hervig, Tor Wee, Joseph T S Nelson, Bradley J Tyler-Smith, Chris van Driem, George Romero, Irene Gallego Jha, Aashish R Karachanak-Yankova, Sena Toncheva, Draga Comas, David Henn, Brenna Kivisild, Toomas Ruiz-Linares, Andres Hormozdiari, Fereydoun Sajantila, Antti Metspalu, Ene Parik, Juri Villems, Richard Starikovskaya, Elena B Ayodo, George Beall, Cynthia M Di Rienzo, Anna Hammer, Michael F Khusainova, Rita Krumm, Niklas Khusnutdinova, Elza Klitz, William Winkler, Cheryl Labuda, Damian Metspalu, Mait Tishkoff, Sarah A Dryomov, Stanislav Sukernik, Rem Patterson, Nick Reich, David Huddleston, John Eichler, Evan E Coe, Bradley P Baker, Carl Nordenfelt, Susanne Bamshad, Michael
Publication Date	2015
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.
Citation	Science, 349(6253), p. 1-9
ISSN	1095-9203 0036-8075
Link	https://hdl.handle.net/1959.11/20607
Language	en
Publisher	American Association for the Advancement of Science (AAAS)
Title	Global diversity, population stratification, and selection of human copy-number variation
Type of document	Journal Article
Entity Type	Publication

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

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