The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Mallick, Swapan; Li, Heng; Skoglund, Pontus; Lazaridis, Iosif; Sankararaman, Sriram; Fu, Qiaomei; Rohland, Nadin; Renaud, Gabriel; Erlich, Yaniv; Willems, Thomas; Gallo, Carla; Spence, Jeffrey P; Lipson, Mark; Song, Yun S; Poletti, Giovanni; Balloux, Francois; van Driem, George; de Knijff, Peter; Romero, Irene Gallego; Jha, Aashish R; Behar, Doron M; Bravi, Claudio M; Capelli, Cristian; Mathieson, Iain; Hervig, Tor; Moreno-Estrada, Andres; Posukh, Olga L; Balanovska, Elena; Balanovsky, Oleg; Karachanak-Yankova, Sena; Sahakyan, Hovhannes; Toncheva, Draga; Yepiskoposyan, Levon; Tyler-Smith, Chris; Gymrek, Melissa; Xue, Yali; Abdullah, M Syafiq; Ruiz-Linares, Andres; Beall, Cynthia M; Di Rienzo, Anna; Jeong, Choongwon; Starikovskaya, Elena B; Metspalu, Ene; Parik, Juri; Villems, Richard; Racimo, Fernando; Henn, Brenna M; Hodoglugil, Ugur; Mahley, Robert; Sajantila, Antti; Stamatoyannopoulos, George; Wee, Joseph T S; Khusainova, Rita; Khusnutdinova, Elza; Litvinov, Sergey; Ayodo, George; Zhao, Mengyao; Comas, David; Hammer, Michael F; Kivisild, Toomas; Klitz, William; Winkler, Cheryl A; Labuda, Damian; Bamshad, Michael; Jorde, Lynn B; Tishkoff, Sarah A; Watkins, W Scott; Chennagiri, Niru; Metspalu, Mait; Dryomov, Stanislav; Sukernik, Rem; Singh, Lalji; Thangaraj, Kumarasamy; Paabo, Svante; Kelso, Janet; Patterson, Nick; Reich, David; Nordenfelt, Susanne; Tandon, Arti

doi:10.1038/nature18964

Author(s)

Mallick, Swapan

Li, Heng

Skoglund, Pontus

Lazaridis, Iosif

Sankararaman, Sriram

Fu, Qiaomei

Rohland, Nadin

Renaud, Gabriel

Erlich, Yaniv

Willems, Thomas

Gallo, Carla

Spence, Jeffrey P

Lipson, Mark

Song, Yun S

Poletti, Giovanni

Balloux, Francois

van Driem, George

de Knijff, Peter

Romero, Irene Gallego

Jha, Aashish R

Behar, Doron M

Bravi, Claudio M

Capelli, Cristian

Mathieson, Iain

Hervig, Tor

Moreno-Estrada, Andres

Posukh, Olga L

Balanovska, Elena

Balanovsky, Oleg

Karachanak-Yankova, Sena

Sahakyan, Hovhannes

Toncheva, Draga

Yepiskoposyan, Levon

Tyler-Smith, Chris

Gymrek, Melissa

Xue, Yali

Abdullah, M Syafiq

Ruiz-Linares, Andres

Beall, Cynthia M

Di Rienzo, Anna

Jeong, Choongwon

Starikovskaya, Elena B

Metspalu, Ene

Parik, Juri

Villems, Richard

Racimo, Fernando

Henn, Brenna M

Hodoglugil, Ugur

Mahley, Robert

Sajantila, Antti

Stamatoyannopoulos, George

Wee, Joseph T S

Khusainova, Rita

Khusnutdinova, Elza

Litvinov, Sergey

Ayodo, George

Zhao, Mengyao

Comas, David

Hammer, Michael F

Kivisild, Toomas

Klitz, William

Winkler, Cheryl A

Labuda, Damian

Bamshad, Michael

Jorde, Lynn B

Tishkoff, Sarah A

Watkins, W Scott

Chennagiri, Niru

Metspalu, Mait

Dryomov, Stanislav

Sukernik, Rem

Singh, Lalji

Thangaraj, Kumarasamy

Paabo, Svante

Kelso, Janet

Patterson, Nick

Reich, David

Nordenfelt, Susanne

Tandon, Arti

Publication Date

2016

Abstract

Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non- Africans.

Citation

Nature, 538(7624), p. 201-206

ISSN

1476-4687

0028-0836

Link

https://hdl.handle.net/1959.11/20757

Language

en

Publisher

Nature Publishing Group

Title

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

Type of document

Journal Article

Entity Type

Publication

Author(s)	Mallick, Swapan Li, Heng Skoglund, Pontus Lazaridis, Iosif Sankararaman, Sriram Fu, Qiaomei Rohland, Nadin Renaud, Gabriel Erlich, Yaniv Willems, Thomas Gallo, Carla Spence, Jeffrey P Lipson, Mark Song, Yun S Poletti, Giovanni Balloux, Francois van Driem, George de Knijff, Peter Romero, Irene Gallego Jha, Aashish R Behar, Doron M Bravi, Claudio M Capelli, Cristian Mathieson, Iain Hervig, Tor Moreno-Estrada, Andres Posukh, Olga L Balanovska, Elena Balanovsky, Oleg Karachanak-Yankova, Sena Sahakyan, Hovhannes Toncheva, Draga Yepiskoposyan, Levon Tyler-Smith, Chris Gymrek, Melissa Xue, Yali Abdullah, M Syafiq Ruiz-Linares, Andres Beall, Cynthia M Di Rienzo, Anna Jeong, Choongwon Starikovskaya, Elena B Metspalu, Ene Parik, Juri Villems, Richard Racimo, Fernando Henn, Brenna M Hodoglugil, Ugur Mahley, Robert Sajantila, Antti Stamatoyannopoulos, George Wee, Joseph T S Khusainova, Rita Khusnutdinova, Elza Litvinov, Sergey Ayodo, George Zhao, Mengyao Comas, David Hammer, Michael F Kivisild, Toomas Klitz, William Winkler, Cheryl A Labuda, Damian Bamshad, Michael Jorde, Lynn B Tishkoff, Sarah A Watkins, W Scott Chennagiri, Niru Metspalu, Mait Dryomov, Stanislav Sukernik, Rem Singh, Lalji Thangaraj, Kumarasamy Paabo, Svante Kelso, Janet Patterson, Nick Reich, David Nordenfelt, Susanne Tandon, Arti
Publication Date	2016
Abstract	Here we report the Simons Genome Diversity Project data set: high quality genomes from 300 individuals from 142 diverse populations. These genomes include at least 5.8 million base pairs that are not present in the human reference genome. Our analysis reveals key features of the landscape of human genome variation, including that the rate of accumulation of mutations has accelerated by about 5% in non-Africans compared to Africans since divergence. We show that the ancestors of some pairs of present-day human populations were substantially separated by 100,000 years ago, well before the archaeologically attested onset of behavioural modernity. We also demonstrate that indigenous Australians, New Guineans and Andamanese do not derive substantial ancestry from an early dispersal of modern humans; instead, their modern human ancestry is consistent with coming from the same source as that of other non- Africans.
Citation	Nature, 538(7624), p. 201-206
ISSN	1476-4687 0028-0836
Link	https://hdl.handle.net/1959.11/20757
Language	en
Publisher	Nature Publishing Group
Title	The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Type of document	Journal Article
Entity Type	Publication

The Simons Genome Diversity Project: 300 genomes from 142 diverse populations

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