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Research Article

Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y

Sandra Wilde, Adrian Timpson, Karola Kirsanow, Elke Kaiser, Manfred Kayser, Martina Unterländer, Nina Hollfelder, Inna D. Potekhina, Wolfram Schier, Mark G. Thomas, and Joachim Burger
PNAS April 1, 2014 111 (13) 4832-4837; https://doi.org/10.1073/pnas.1316513111
Sandra Wilde
aInstitute of Anthropology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
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Adrian Timpson
bResearch Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom;cInstitute of Archaeology, University College London, London WC1H 0PY, United Kingdom;
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Karola Kirsanow
aInstitute of Anthropology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
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Elke Kaiser
dInstitute of Prehistoric Archaeology, Freie Universität Berlin, 14195 Berlin, Germany;
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Manfred Kayser
eDepartment of Forensic Molecular Biology, Erasmus University Medical Center Rotterdam, 3000 CA, Rotterdam, The Netherlands; and
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Martina Unterländer
aInstitute of Anthropology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
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Nina Hollfelder
aInstitute of Anthropology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
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Inna D. Potekhina
fInstitute of Archaeology, Academy of Science of the Ukraine, 04210 Kiev-210, Ukraine
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Wolfram Schier
dInstitute of Prehistoric Archaeology, Freie Universität Berlin, 14195 Berlin, Germany;
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Mark G. Thomas
bResearch Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom;
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  • For correspondence: m.thomas@ucl.ac.uk
Joachim Burger
aInstitute of Anthropology, Johannes Gutenberg University Mainz, 55128 Mainz, Germany;
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  1. Edited by Nina G. Jablonski, The Pennsylvania State University, University Park, Pennsylvania, and accepted by the Editorial Board February 1, 2014 (received for review September 4, 2013)

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    Fig. 1.

    Probabilities of obtaining FST equal to or greater than that observed (0.00551) between 60 Eneolithic (ca. 6,500–5,000 y ago) and Bronze Age (ca. 5,000–4,000 y ago) samples from the Pontic–Caspian steppe, and a combined sample of 246 homologous modern sequences from the same geographic region, across a range of assumed ancestral population size combinations. Two phases of exponential growth were modeled, the first after the initial colonization of Europe 45,000 y ago, of assumed effective female population size NUP (y axis), and ending when farming began in the region considered 7,000 y ago, when the assumed effective female population size was NN (x axis), and the second leading up to the present, when the assumed effective female population size is 5,444,812. The initial colonizers of Europe were sampled from a constant ancestral African population of 5,000 effective females. Gray shaded areas indicate P values >0.05.

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    Fig. 2.

    Two-tailed empirical P values for obtaining the observed (A) SLC45A2 G allele, (B) TYR A allele, and (C) HERC2 G allele frequency increase. P values were obtained by forward simulation of drift and natural selection across a range of assumed ancestral population sizes and selection coefficients, assuming exponential growth to a modern Ne of 4,845,710. The SLC45A2 rs16891982 G allele and the TYR rs1042602 A allele were assumed to be codominant. The HERC2 rs12913832 G allele was assumed to be recessive (values less than 0.01 are shaded gray).

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    Table 1.

    Allele frequencies of three functional SNPs associated with pigmentation in ancient and modern populations

    Derived allele frequency
    GeneSNPPolymorphismEuropeAsiaAfricaModern Ukrainian sampleAncient sample
    HERC2rs12913832 regulatory element (OCA2)A > G0.710 [758]0.002 [572]0.000 [370]0.651 (0.546–0.744) [86]0.160 (0.099–0.247) [94]
    SLC45A2 (MATP)rs16891982 Leu374PheC > G0.970 [758]0.007 [572]0.000 [370]0.927 (0.849–0.965) [82]0.432 (0.296–0.578) [44]
    TYRrs1042602 Ser192TyrC > A0.368 [758]0.002 [572]0.000 [370]0.367 (0.279–0.466) [98]0.043 (0.018–0.106) [92]
    • Modern allele frequencies are from 1000 Genomes (http://browser.1000genomes.org) (65). Range in parentheses indicates the equal-tailed 95% confidence interval calculated as described using the qbeta function in R (66). Numbers in square brackets indicate 2N individuals. The African American (ASW) data from 1000 Genomes were excluded because this population is admixed to an unknown extent.

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Direct evidence for selection on pigmentation
Sandra Wilde, Adrian Timpson, Karola Kirsanow, Elke Kaiser, Manfred Kayser, Martina Unterländer, Nina Hollfelder, Inna D. Potekhina, Wolfram Schier, Mark G. Thomas, Joachim Burger
Proceedings of the National Academy of Sciences Apr 2014, 111 (13) 4832-4837; DOI: 10.1073/pnas.1316513111

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Direct evidence for selection on pigmentation
Sandra Wilde, Adrian Timpson, Karola Kirsanow, Elke Kaiser, Manfred Kayser, Martina Unterländer, Nina Hollfelder, Inna D. Potekhina, Wolfram Schier, Mark G. Thomas, Joachim Burger
Proceedings of the National Academy of Sciences Apr 2014, 111 (13) 4832-4837; DOI: 10.1073/pnas.1316513111
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