Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

The demographic history and mutational load of African hunter-gatherers and farmers

Marie Lopez, Athanasios Kousathanas, Hélène Quach, Christine Harmant, Patrick Mouguiama-Daouda, Jean-Marie Hombert, Alain Froment, George H. Perry, Luis B. Barreiro, Paul Verdu, Etienne Patin, Lluís Quintana-Murci
doi: https://doi.org/10.1101/131219
Marie Lopez
aHuman Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
bCentre National de la Recherche Scientifique (CNRS) URA3012, 75015 Paris, France
cCenter of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Athanasios Kousathanas
aHuman Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
bCentre National de la Recherche Scientifique (CNRS) URA3012, 75015 Paris, France
cCenter of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hélène Quach
aHuman Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
bCentre National de la Recherche Scientifique (CNRS) URA3012, 75015 Paris, France
cCenter of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Christine Harmant
aHuman Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
bCentre National de la Recherche Scientifique (CNRS) URA3012, 75015 Paris, France
cCenter of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Patrick Mouguiama-Daouda
dLaboratoire Langue, Culture et Cognition (LCC), Université Omar Bongo, BP 13131 Libreville, Gabon
eCNRS UMR 5596, Dynamique du Langage, Université Lumière-Lyon 2, 69007 Lyon, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jean-Marie Hombert
eCNRS UMR 5596, Dynamique du Langage, Université Lumière-Lyon 2, 69007 Lyon, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Alain Froment
fInstitut de Recherche pour le Développement UMR 208, Muséum National d’Histoire Naturelle, 75005 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
George H. Perry
gDepartments of Anthropology and Biology, Pennsylvania State University, University Park, PA 16802, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Luis B. Barreiro
hUniversité de Montréal, Centre de Recherche CHU Sainte-Justine, H3T 1C5 Montréal, Canada
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Paul Verdu
iCNRS UMR7206, Muséum National d’Histoire Naturelle, Université Paris Diderot, Sorbonne Paris Cité, Paris 75016, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Etienne Patin
aHuman Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
bCentre National de la Recherche Scientifique (CNRS) URA3012, 75015 Paris, France
cCenter of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Lluís Quintana-Murci
aHuman Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
bCentre National de la Recherche Scientifique (CNRS) URA3012, 75015 Paris, France
cCenter of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, 75015 Paris, France
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

The distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains to be fully characterized. We addressed this question, by generating 300 high-coverage exome sequences from various populations of rainforest hunter-gatherers and neighboring farmers from the western and eastern parts of the central African equatorial rainforest. We show here, by model-based demographic inference, that the effective population size of African populations remained fairly constant until recent millennia, during which the populations of rainforest hunter-gatherers have experienced a ∼75% collapse and those of farmers a mild expansion, accompanied by a marked increase in gene flow between them. Despite these contrasting demographic patterns, African populations display limited differences in the estimated distribution of fitness effects of new nonsynonymous mutations, consistent with purifying selection against deleterious alleles of similar efficiency in the different populations. This situation contrasts with that we detect in Europeans, which are subject to weaker purifying selection than African populations. Furthermore, the per-individual mutation load of rainforest hunter-gatherers was found to be similar to that of farmers, under both additive and recessive modes of inheritance. Together, our results indicate that differences in the subsistence patterns and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

Significance Statement The last 100,000 years of human history have been characterized by important demographic events, including population splits, size changes and gene flow, potentially affecting the distribution of deleterious mutations across populations and, ultimately, disease risk. We sequenced the exomes of various African rainforest hunter-gatherer and sedentary farming populations, reconstructed their demographic histories, and explored the effects of differences in lifestyles and demography on mutational load. We found that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and population expansions for farmers. However, these contrasted pasts have not translated into major differences in the efficiency of purifying selection against deleterious alleles, leading to a similar mutational burden in the two groups.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted April 26, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
The demographic history and mutational load of African hunter-gatherers and farmers
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
The demographic history and mutational load of African hunter-gatherers and farmers
Marie Lopez, Athanasios Kousathanas, Hélène Quach, Christine Harmant, Patrick Mouguiama-Daouda, Jean-Marie Hombert, Alain Froment, George H. Perry, Luis B. Barreiro, Paul Verdu, Etienne Patin, Lluís Quintana-Murci
bioRxiv 131219; doi: https://doi.org/10.1101/131219
Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
Citation Tools
The demographic history and mutational load of African hunter-gatherers and farmers
Marie Lopez, Athanasios Kousathanas, Hélène Quach, Christine Harmant, Patrick Mouguiama-Daouda, Jean-Marie Hombert, Alain Froment, George H. Perry, Luis B. Barreiro, Paul Verdu, Etienne Patin, Lluís Quintana-Murci
bioRxiv 131219; doi: https://doi.org/10.1101/131219

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Evolutionary Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (4655)
  • Biochemistry (10307)
  • Bioengineering (7618)
  • Bioinformatics (26203)
  • Biophysics (13453)
  • Cancer Biology (10625)
  • Cell Biology (15348)
  • Clinical Trials (138)
  • Developmental Biology (8456)
  • Ecology (12761)
  • Epidemiology (2067)
  • Evolutionary Biology (16777)
  • Genetics (11361)
  • Genomics (15407)
  • Immunology (10556)
  • Microbiology (25060)
  • Molecular Biology (10162)
  • Neuroscience (54128)
  • Paleontology (398)
  • Pathology (1655)
  • Pharmacology and Toxicology (2877)
  • Physiology (4315)
  • Plant Biology (9204)
  • Scientific Communication and Education (1582)
  • Synthetic Biology (2543)
  • Systems Biology (6753)
  • Zoology (1453)