The genomic footprint of social stratification in admixing American populations

  1. Alex Mas Sandoval  Is a corresponding author
  2. Sara Mathieson
  3. Matteo Fumagalli  Is a corresponding author
  1. Imperial College London, United Kingdom
  2. Haverford College, United States

Abstract

Cultural and socioeconomic differences stratify human societies and shape their genetic structure beyond the sole effect of geography. Despite mating being limited by sociocultural stratification, most demographic models in population genetics often assume random mating. Taking advantage of the correlation between sociocultural stratification and the proportion of genetic ancestry in admixed populations, we sought to infer the former process in the Americas. To this aim, we define a mating model where the individual proportions of the genome inherited from Native American, European and sub-Saharan African ancestral populations constrain the mating probabilities through ancestry-related assortative mating and sex bias parameters. We simulate a wide range of admixture scenarios under this model. Then, we train a deep neural network and retrieve good performance in predicting mating parameters from genomic data. Our results show how population stratification shaped by socially constructed racial and gender hierarchies have constrained the admixture processes in the Americas since the European colonisation and the subsequent Atlantic slave trade.

Data availability

The current manuscript uses already published data, so no data have been generated for this manuscript. The code used for the computational analyses is made available at the address stated in the methods.

The following previously published data sets were used

Article and author information

Author details

  1. Alex Mas Sandoval

    Department of Life Sciences, Imperial College London, Ascot, United Kingdom
    For correspondence
    alex.massandoval@unibo.it
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1712-9404
  2. Sara Mathieson

    Department of Computer Science, Haverford College, Haverford, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0484-0838
  3. Matteo Fumagalli

    Department of Life Sciences, Imperial College London, Ascot, United Kingdom
    For correspondence
    m.fumagalli@qmul.ac.uk
    Competing interests
    The authors declare that no competing interests exist.

Funding

Leverhulme Trust (RPG-2018-208)

  • Alex Mas Sandoval
  • Matteo Fumagalli

National Institutes of Health (R15HG011528)

  • Sara Mathieson

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Emilia Huerta-Sanchez, Brown University, United States

Version history

  1. Received: October 24, 2022
  2. Preprint posted: November 18, 2022 (view preprint)
  3. Accepted: November 22, 2023
  4. Accepted Manuscript published: December 1, 2023 (version 1)
  5. Version of Record published: January 9, 2024 (version 2)

Copyright

© 2023, Mas Sandoval et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Alex Mas Sandoval
  2. Sara Mathieson
  3. Matteo Fumagalli
(2023)
The genomic footprint of social stratification in admixing American populations
eLife 12:e84429.
https://doi.org/10.7554/eLife.84429

Share this article

https://doi.org/10.7554/eLife.84429

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