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A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers

Human Genetics volume 137, pages 487–509 (2018)Cite this article

Abstract

The evolutionary and biological bases of the Central African “pygmy” phenotype, a characteristic of rainforest hunter-gatherers defined by reduced body size compared with neighboring farmers, remain largely unknown. Here, we perform a joint investigation in Central African hunter-gatherers and farmers of adult standing height, sitting height, leg length, and body mass index (BMI), considering 358 hunter-gatherers and 169 farmers with genotypes for 153,798 SNPs. In addition to reduced standing heights, hunter-gatherers have shorter sitting heights and leg lengths and higher sitting/standing height ratios than farmers and lower BMI for males. Standing height, sitting height, and leg length are strongly correlated with inferred levels of farmer genetic ancestry, whereas BMI is only weakly correlated, perhaps reflecting greater contributions of non-genetic factors to body weight than to height. Single- and multi-marker association tests identify one region and eight genes associated with hunter-gatherer/farmer status, and 24 genes associated with the height-related traits. Many of these genes have putative functions consistent with roles in determining their associated traits and the pygmy phenotype, and they include three associated with standing height in non-Africans (PRKG1, DSCAM, MAGI2). We find evidence that European height-associated SNPs or variants in linkage disequilibrium with them contribute to standing- and sitting-height determination in Central Africans, but not to the differential status of hunter-gatherers and farmers. These findings provide new insights into the biological basis of the pygmy phenotype, and they highlight the potential of cross-population studies for exploring the genetic basis of phenotypes that vary naturally across populations.

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Acknowledgements

The authors thank the volunteers from Cameroon, Central African Republic, Gabon, and Uganda who participated in this study. They thank Peter Chines for providing independently verified Cardio-MetaboChip SNP positions, Sen Li for providing ancestral and derived allelic states for the MetaboChip SNPs, Hyun Min Kang for EMMAX assistance, and Frédéric Austerlitz, Erkan Buzbas, Zachary Szpiech, and Lawrence Uricchio for useful comments and discussions. This investigation was supported by the France-Stanford Center for Interdisciplinary Studies (N. A. R.); the French Assistance Publique Hôpitaux de Paris, ATM-MNHN ‘Les relations Sociétés-Natures dans le long terme’ 2009–2012 and the Fondation pour la Recherche Médicale and the ANR-Blanc program ‘GrowingAP’ (E. H.); a University of Michigan Center for Genetics in Health and Medicine postdoctoral fellowship (T. J. P.); and a Natural Sciences and Engineering Research Council of Canada Discovery Grant (RGPIN-2015-04739; T. J. P.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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Author notes

  1. Trevor J. Pemberton and Paul Verdu contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada

    Trevor J. Pemberton

  2. CNRS-MNHN-Université Paris Diderot, UMR 7206 Eco-Anthropologie et Ethnobiologie, Paris, France

    Paul Verdu, Sylvie Le Bomin & Evelyne Heyer

  3. Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany

    Noémie S. Becker

  4. Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI, USA

    Cristen J. Willer

  5. Department of Anthropology, Washington State University, Vancouver, WA, USA

    Barry S. Hewlett

  6. IRD–MNHN, UMR 208 Patrimoines locaux, Paris, France

    Alain Froment

  7. Department of Biology, Stanford University, Stanford, CA, USA

    Noah A. Rosenberg

Authors
  1. Trevor J. Pemberton
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  9. Evelyne Heyer
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Corresponding authors

Correspondence to Trevor J. Pemberton, Paul Verdu, Noah A. Rosenberg or Evelyne Heyer.

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Ethics approval and consent to participate

The study was conducted according to ethical principles of the Declaration of Helsinki. IRB approvals were obtained from the French Ministry of Higher Education and Research (2005, renewed in 2010 and 2016), Stanford (2012) and Washington State Universities (2007), and the Universities of Manitoba (2013) and Michigan (2010). Prior to sample collection, research authorizations were obtained from the Ministry of Public Health in Cameroon (2005; renewed 2010), the Ministry of Higher Education and Research in Gabon (2006 and 2007), the National Council for Science and Technology in Uganda (2007), and the Ministry of Scientific Research in the Central African Republic (2007). Informed consent was obtained from all participants.

Conflict of interest

The authors declare that they have no conflicts of interest.

Availability of data and material

The Illumina Cardio-MetaboChip SNP genotype datasets for the 406 unrelated individuals analyzed are available in the European Genome-Phenome archive (EGAS00001002975) and will be accessible for population-genetic studies of demography and natural selection as well as for anthropological-genetic studies of the genetic determination of anthropometrical phenotypic features in accordance with the informed consent documents used in the recruitment of individuals who participated in this study.

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Pemberton, T.J., Verdu, P., Becker, N.S. et al. A genome scan for genes underlying adult body size differences between Central African hunter-gatherers and farmers. Hum Genet 137, 487–509 (2018). https://doi.org/10.1007/s00439-018-1902-3

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