Reconstructing Prehistoric African Population Structure

Pontus Skoglund; Jessica C. Thompson; Mary E. Prendergast; Alissa Mittnik; Kendra Sirak; Mateja Hajdinjak; Tasneem Salie; Nadin Rohland; Swapan Mallick; Alexander Peltzer; Anja Heinze; Iñigo Olalde; Matthew Ferry; Eadaoin Harney; Megan Michel; Kristin Stewardson; Jessica I. Cerezo-Román; Chrissy Chiumia; Alison Crowther; Elizabeth Gomani-Chindebvu; Agness O. Gidna; Katherine M. Grillo; I. Taneli Helenius; Garrett Hellenthal; Richard Helm; Mark Horton; Saioa López; Audax Z.P. Mabulla; John Parkington; Ceri Shipton; Mark G. Thomas; Ruth Tibesasa; Menno Welling; Vanessa M. Hayes; Douglas J. Kennett; Raj Ramesar; Matthias Meyer; Svante Pääbo; Nick Patterson; Alan G. Morris; Nicole Boivin; Ron Pinhasi; Johannes Krause; David Reich

doi:10.1016/j.cell.2017.08.049

Reconstructing Prehistoric African Population Structure

Pontus Skoglund, Jessica C. Thompson, Mary E. Prendergast, Alissa Mittnik, Kendra Sirak, Mateja Hajdinjak, Tasneem Salie, Nadin Rohland, Swapan Mallick, Alexander Peltzer, Anja Heinze, Iñigo Olalde, Matthew Ferry, Eadaoin Harney, Megan Michel, Kristin Stewardson, Jessica I. Cerezo-Román, Chrissy Chiumia, Alison Crowther, Elizabeth Gomani-ChindebvuAgness O. Gidna, Katherine M. Grillo, I. Taneli Helenius, Garrett Hellenthal, Richard Helm, Mark Horton, Saioa López, Audax Z.P. Mabulla, John Parkington, Ceri Shipton, Mark G. Thomas, Ruth Tibesasa, Menno Welling, Vanessa M. Hayes, Douglas J. Kennett, Raj Ramesar, Matthias Meyer, Svante Pääbo, Nick Patterson, Alan G. Morris, Nicole Boivin, Ron Pinhasi, Johannes Krause, David Reich

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

260 Scopus citations

Abstract

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

Original language	English (US)
Pages (from-to)	59-71.e21
Journal	Cell
Volume	171
Issue number	1
DOIs	https://doi.org/10.1016/j.cell.2017.08.049
State	Published - Sep 21 2017

All Science Journal Classification (ASJC) codes

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.cell.2017.08.049

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Skoglund, P., Thompson, J. C., Prendergast, M. E., Mittnik, A., Sirak, K., Hajdinjak, M., Salie, T., Rohland, N., Mallick, S., Peltzer, A., Heinze, A., Olalde, I., Ferry, M., Harney, E., Michel, M., Stewardson, K., Cerezo-Román, J. I., Chiumia, C., Crowther, A., ... Reich, D. (2017). Reconstructing Prehistoric African Population Structure. Cell, 171(1), 59-71.e21. https://doi.org/10.1016/j.cell.2017.08.049

@article{1db1058f495941e381643f053c17290f,

title = "Reconstructing Prehistoric African Population Structure",

abstract = "We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.",

author = "Pontus Skoglund and Thompson, {Jessica C.} and Prendergast, {Mary E.} and Alissa Mittnik and Kendra Sirak and Mateja Hajdinjak and Tasneem Salie and Nadin Rohland and Swapan Mallick and Alexander Peltzer and Anja Heinze and I{\~n}igo Olalde and Matthew Ferry and Eadaoin Harney and Megan Michel and Kristin Stewardson and Cerezo-Rom{\'a}n, {Jessica I.} and Chrissy Chiumia and Alison Crowther and Elizabeth Gomani-Chindebvu and Gidna, {Agness O.} and Grillo, {Katherine M.} and Helenius, {I. Taneli} and Garrett Hellenthal and Richard Helm and Mark Horton and Saioa L{\'o}pez and Mabulla, {Audax Z.P.} and John Parkington and Ceri Shipton and Thomas, {Mark G.} and Ruth Tibesasa and Menno Welling and Hayes, {Vanessa M.} and Kennett, {Douglas J.} and Raj Ramesar and Matthias Meyer and Svante P{\"a}{\"a}bo and Nick Patterson and Morris, {Alan G.} and Nicole Boivin and Ron Pinhasi and Johannes Krause and David Reich",

note = "Publisher Copyright: {\textcopyright} 2017 Elsevier Inc.",

year = "2017",

month = sep,

day = "21",

doi = "10.1016/j.cell.2017.08.049",

language = "English (US)",

volume = "171",

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Skoglund, P, Thompson, JC, Prendergast, ME, Mittnik, A, Sirak, K, Hajdinjak, M, Salie, T, Rohland, N, Mallick, S, Peltzer, A, Heinze, A, Olalde, I, Ferry, M, Harney, E, Michel, M, Stewardson, K, Cerezo-Román, JI, Chiumia, C, Crowther, A, Gomani-Chindebvu, E, Gidna, AO, Grillo, KM, Helenius, IT, Hellenthal, G, Helm, R, Horton, M, López, S, Mabulla, AZP, Parkington, J, Shipton, C, Thomas, MG, Tibesasa, R, Welling, M, Hayes, VM, Kennett, DJ, Ramesar, R, Meyer, M, Pääbo, S, Patterson, N, Morris, AG, Boivin, N, Pinhasi, R, Krause, J & Reich, D 2017, 'Reconstructing Prehistoric African Population Structure', Cell, vol. 171, no. 1, pp. 59-71.e21. https://doi.org/10.1016/j.cell.2017.08.049

TY - JOUR

T1 - Reconstructing Prehistoric African Population Structure

AU - Skoglund, Pontus

AU - Thompson, Jessica C.

AU - Prendergast, Mary E.

AU - Mittnik, Alissa

AU - Sirak, Kendra

AU - Hajdinjak, Mateja

AU - Salie, Tasneem

AU - Rohland, Nadin

AU - Mallick, Swapan

AU - Peltzer, Alexander

AU - Heinze, Anja

AU - Olalde, Iñigo

AU - Ferry, Matthew

AU - Harney, Eadaoin

AU - Michel, Megan

AU - Stewardson, Kristin

AU - Cerezo-Román, Jessica I.

AU - Chiumia, Chrissy

AU - Crowther, Alison

AU - Gomani-Chindebvu, Elizabeth

AU - Gidna, Agness O.

AU - Grillo, Katherine M.

AU - Helenius, I. Taneli

AU - Hellenthal, Garrett

AU - Helm, Richard

AU - Horton, Mark

AU - López, Saioa

AU - Mabulla, Audax Z.P.

AU - Parkington, John

AU - Shipton, Ceri

AU - Thomas, Mark G.

AU - Tibesasa, Ruth

AU - Welling, Menno

AU - Hayes, Vanessa M.

AU - Kennett, Douglas J.

AU - Ramesar, Raj

AU - Meyer, Matthias

AU - Pääbo, Svante

AU - Patterson, Nick

AU - Morris, Alan G.

AU - Boivin, Nicole

AU - Pinhasi, Ron

AU - Krause, Johannes

AU - Reich, David

PY - 2017/9/21

Y1 - 2017/9/21

N2 - We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

AB - We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations.

UR - http://www.scopus.com/inward/record.url?scp=85029625888&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85029625888&partnerID=8YFLogxK

U2 - 10.1016/j.cell.2017.08.049

DO - 10.1016/j.cell.2017.08.049

M3 - Article

C2 - 28938123

AN - SCOPUS:85029625888

SN - 0092-8674

VL - 171

SP - 59-71.e21

JO - Cell

JF - Cell

IS - 1

ER -

Reconstructing Prehistoric African Population Structure

Abstract

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