Native American genetic ancestry and pigmentation allele contributions to skin color in a caribbean population
- Pennsylvania State University, United States
- Salybia Mission Project, Dominica
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.
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Native American Genetic Ancestry and Pigmentation Allele Contributions to Skin Color in a Caribbean PopulationDryad Digital Repository, doi:10.5061/dryad.sf7m0cg7z.
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A map of human genome variation from population-scale sequencinghttps://www.internationalgenome.org/data.
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Reconstructing Native American population historydoi:10.1038/nature11258.
Article and author information
Author details
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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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
Further reading
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- Evolutionary Biology
The majority of highly polymorphic genes are related to immune functions and with over 100 alleles within a population, genes of the major histocompatibility complex (MHC) are the most polymorphic loci in vertebrates. How such extraordinary polymorphism arose and is maintained is controversial. One possibility is heterozygote advantage (HA), which can in principle maintain any number of alleles, but biologically explicit models based on this mechanism have so far failed to reliably predict the coexistence of significantly more than 10 alleles. We here present an eco-evolutionary model showing that evolution can result in the emergence and maintenance of more than 100 alleles under HA if the following two assumptions are fulfilled: first, pathogens are lethal in the absence of an appropriate immune defence; second, the effect of pathogens depends on host condition, with hosts in poorer condition being affected more strongly. Thus, our results show that HA can be a more potent force in explaining the extraordinary polymorphism found at MHC loci than currently recognised.
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