Native American genetic ancestry and pigmentation allele contributions to skin color in a caribbean population

Abstract

Our interest in the genetic basis of skin color variation between populations led us to seek a Native American population with genetically African admixture but low frequency of European light skin alleles. Analysis of 458 genomes from individuals residing in the Kalinago territory of the Commonwealth of Dominica showed approximately 55% Native American, 32% African, and 12% European genetic ancestry, the highest Native American genetic ancestry among Caribbean populations to date. Skin pigmentation ranged from 20 to 80 melanin units, averaging 46. Three albino individuals were determined to be homozygous for a causative multi-nucleotide polymorphism OCA2NW273KV contained within a haplotype of African origin; its allele frequency was 0.03 and single allele effect size was -8 melanin units. Derived allele frequencies of SLC24A5A111T and SLC45A2L374F were 0.14 and 0.06, with single allele effect sizes of -6 and -4, respectively. Native American genetic ancestry by itself reduced pigmentation by more than 20 melanin units (range 24 - 29). The responsible hypopigmenting genetic variants remain to be identified, since none of the published polymorphisms predicted in prior literature to affect skin color in Native Americans caused detectable hypopigmentation in the Kalinago.

Data availability

The whole exome sequencing and whole genome SNP genotyping data underlying this article cannot be shared publicly due to the privacy of individuals and stipulation by the Kalinago community. Only de-identified filtered SNP data used in analyses will be shared. Additional data will be shared on request to the corresponding author, pending approval from the Kalinago Council.M-index and specific genotyping data (SLC24A5 A111T, SLC45A2 L374F, OCA2 NW273KV and OCA2 305W) and genotyping data for Admixture have been uploaded to Dryad https://doi.org/10.5061/dryad.sf7m0cg7zThe data cannot be used for any commercial purposes.We did not create any new software or script for analysis.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Khai C Ang

    Department of Pathology, Pennsylvania State University, Hershey, United States
    For correspondence
    kca2@psu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7695-9953
  2. Victor A Canfield

    Department of Pathology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Tiffany C Foster

    Department of Pathology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Thaddeus D Harbaugh

    Department of Pathology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Kathryn A Early

    Department of Pathology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Rachel L Harter

    Department of Pathology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Katherine P Reid

    Department of Pathology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Shou Ling Leong

    Department of Family and Community Medicine, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Yuka Kawasawa

    Department of Pharmacology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8638-6738
  10. Dajiang Liu

    Department of Biochemistry and Molecular Biology, Pennsylvania State University, Hershey, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. John W Hawley

    Salybia Mission Project, Portsmouth, Dominica
    Competing interests
    The authors declare that no competing interests exist.
  12. Keith C Cheng

    Jake Gittlen Laboratories for Cancer Research, Pennsylvania State University, Hershey, United States
    For correspondence
    kcheng76@gmail.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5350-5825

Funding

Hershey Rotary Club

  • Khai C Ang

Jake Gittlen Laboratories for Cancer Research

  • Keith C Cheng

Penn State College of Medicine Department of Pathology

  • Keith C Cheng

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

Ethics

Human subjects: The study was reviewed and approved by the Kalinago council and institutional review boards of Penn State University (29269EP), Ross University, and the Dominica Ministry of Health (H125). Informed consent was obtained from each participant enrolled in the study, and in the case of minors, consent was also obtained from a parent or guardian.

Copyright

© 2023, Ang 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. Khai C Ang
  2. Victor A Canfield
  3. Tiffany C Foster
  4. Thaddeus D Harbaugh
  5. Kathryn A Early
  6. Rachel L Harter
  7. Katherine P Reid
  8. Shou Ling Leong
  9. Yuka Kawasawa
  10. Dajiang Liu
  11. John W Hawley
  12. Keith C Cheng
(2023)
Native American genetic ancestry and pigmentation allele contributions to skin color in a caribbean population
eLife 12:e77514.
https://doi.org/10.7554/eLife.77514

Share this article

https://doi.org/10.7554/eLife.77514

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