Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

Joseph Lachance; Benjamin Vernot; Clara C. Elbers; Bart Ferwerda; Alain Froment; Jean Marie Bodo; Godfrey Lema; Wenqing Fu; Thomas B. Nyambo; Timothy R. Rebbeck; Kun Zhang; Joshua M. Akey; Sarah A. Tishkoff

doi:10.1016/j.cell.2012.07.009

Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

Joseph Lachance, Benjamin Vernot, Clara C. Elbers, Bart Ferwerda, Alain Froment, Jean Marie Bodo, Godfrey Lema, Wenqing Fu, Thomas B. Nyambo, Timothy R. Rebbeck, Kun Zhang, Joshua M. Akey, Sarah A. Tishkoff

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

221 Scopus citations

Abstract

To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60× coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.

Original language	English (US)
Pages (from-to)	457-469
Number of pages	13
Journal	Cell
Volume	150
Issue number	3
DOIs	https://doi.org/10.1016/j.cell.2012.07.009
State	Published - Aug 3 2012
Externally published	Yes

All Science Journal Classification (ASJC) codes

General Biochemistry, Genetics and Molecular Biology

Access to Document

10.1016/j.cell.2012.07.009

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@article{60d0b90a46184f0b959d394e11236a8d,

title = "Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers",

abstract = "To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60× coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.",

author = "Joseph Lachance and Benjamin Vernot and Elbers, {Clara C.} and Bart Ferwerda and Alain Froment and Bodo, {Jean Marie} and Godfrey Lema and Wenqing Fu and Nyambo, {Thomas B.} and Rebbeck, {Timothy R.} and Kun Zhang and Akey, {Joshua M.} and Tishkoff, {Sarah A.}",

note = "Funding Information: This work was supported by NSF (BCS-0827436) and NIH (R01GM076637, 8 DP1 ES022577-04) grants to S.A.T., an NIH NRSA postdoctoral fellowship (F32HG006648-01) to J.L., Rubicon Grants of the Netherlands Organization of Scientific Research to C.C.E. and B.F., and support from the Center of Excellence in Environmental Toxicology at the University of Pennsylvania, P30-ES013508-07. We thank J. Hirbo, J. Jarvis, A. Rawlings, L. Scheinfeld, and S. Soi for their critical feedback and advice and K. Addya, D. Baldwin, and B. Beggs for assistance in genotyping the samples. We also thank the 15 individuals who graciously supplied their DNA. ",

year = "2012",

month = aug,

day = "3",

doi = "10.1016/j.cell.2012.07.009",

language = "English (US)",

volume = "150",

pages = "457--469",

journal = "Cell",

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publisher = "Elsevier B.V.",

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T1 - Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

AU - Lachance, Joseph

AU - Vernot, Benjamin

AU - Elbers, Clara C.

AU - Ferwerda, Bart

AU - Froment, Alain

AU - Bodo, Jean Marie

AU - Lema, Godfrey

AU - Fu, Wenqing

AU - Nyambo, Thomas B.

AU - Rebbeck, Timothy R.

AU - Zhang, Kun

AU - Akey, Joshua M.

AU - Tishkoff, Sarah A.

N1 - Funding Information: This work was supported by NSF (BCS-0827436) and NIH (R01GM076637, 8 DP1 ES022577-04) grants to S.A.T., an NIH NRSA postdoctoral fellowship (F32HG006648-01) to J.L., Rubicon Grants of the Netherlands Organization of Scientific Research to C.C.E. and B.F., and support from the Center of Excellence in Environmental Toxicology at the University of Pennsylvania, P30-ES013508-07. We thank J. Hirbo, J. Jarvis, A. Rawlings, L. Scheinfeld, and S. Soi for their critical feedback and advice and K. Addya, D. Baldwin, and B. Beggs for assistance in genotyping the samples. We also thank the 15 individuals who graciously supplied their DNA.

PY - 2012/8/3

Y1 - 2012/8/3

N2 - To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60× coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.

AB - To reconstruct modern human evolutionary history and identify loci that have shaped hunter-gatherer adaptation, we sequenced the whole genomes of five individuals in each of three different hunter-gatherer populations at >60× coverage: Pygmies from Cameroon and Khoesan-speaking Hadza and Sandawe from Tanzania. We identify 13.4 million variants, substantially increasing the set of known human variation. We found evidence of archaic introgression in all three populations, and the distribution of time to most recent common ancestors from these regions is similar to that observed for introgressed regions in Europeans. Additionally, we identify numerous loci that harbor signatures of local adaptation, including genes involved in immunity, metabolism, olfactory and taste perception, reproduction, and wound healing. Within the Pygmy population, we identify multiple highly differentiated loci that play a role in growth and anterior pituitary function and are associated with height.

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JO - Cell

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ER -

Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers

Abstract

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