Comparing signals of natural selection between three Indigenous North American populations
Open accessAbstract
While many studies have highlighted human adaptations to diverse environments worldwide, genomic studies of natural selection in Indigenous populations in the Americas have been absent from this literature until very recently. Since humans first entered the Americas some 20,000 years ago, they have settled in many new environments across the continent. This diversity of environments has placed variable selective pressures on the populations living in each region, but the effects of these pressures have not been extensively studied to date. To help fill this gap, we collected genome-wide data from three Indigenous North American populations from different geographic regions of the continent (Alaska, southeastern United States, and central Mexico). We identified signals of natural selection in each population and compared signals across populations to explore the differences in selective pressures among the three regions sampled. We find evidence of adaptation to cold and high-latitude environments in Alaska, while in the southeastern United States and central Mexico, pathogenic environments seem to have created important selective pressures. This study lays the foundation for additional functional and phenotypic work on possible adaptations to varied environments during the history of population diversification in the Americas.
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Some of the regions with high-frequency archaic alleles contain genes already identified as adaptively introgressed in Indigenous American populations, including IFIH1/FAP and WARS2 in PEL, and LRRK2/MUC19 in MXL.
“Some of these regions contain genes that have already been identified as adaptively introgressed in Indigenous American populations, including IFIH1/FAP (Ávila-Arcos et al. 2020) and WARS2 (Racimo et al. 2018), identified in PEL, and LRRK2/MUC19 (Reynolds et al. 2019), identified in MXL.”
From The Impact of Modern Admixture on Archaic Human Ancestry in Human Populations (2023) · cites this paper as Reynolds et al. 2019
The Discussion (page unavailable) reports a strong signal of selection at MUC19 in the central Mexico population. It does not identify the signal as adaptive archaic introgression or report it for MXL; the retrieved passages also do not identify LRRK2 as a selected gene. (LLM, conf=0.87)
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Self-citationZakai, S. (2018) · Routledge eBooks · doi:10.4324/9781315110646-7 · Cited by 2 · see citing works
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A Tale of Native American Whole-Genome Sequencing and Other Technologies
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Loma, J. D., Vicente, M., Tirado, N., Ascui, F., Parada, L. A., Gardon, J., Schlebusch, C. M., & Bröberg, K. (2025) · Human Population Genetics and Genomics · doi:10.47248/hpgg2505010002 · Cited by 1 · see citing works
Malyarchuk, B. А. (2023) · Vavilov Journal of Genetics and Breeding · doi:10.18699/vjgb-23-45 · Cited by 1 · see citing works
Homo anxius, or How Fear and Anxiety Conquered the Social World
Ambasciano, L. (2022) · Journal of Cognitive Historiography · doi:10.1558/jch.19349
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Meltzer, D. J. (2021) · Cambridge University Press eBooks · doi:10.1017/9781108632867.010
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Meltzer, D. J. (2021) · Cambridge University Press eBooks · doi:10.1017/9781108632867.015
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Who, from Where, When, and How?
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Ascertaining Archaeological Evidence of Antiquity
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Shamanism Yesterday, Today, and Tomorrow
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- Authors
- Reynolds, A. W., Mata-Míguez, J., Miró-Herrans, A., Briggs-Cloud, M., Sylestine, A., Barajas-Olmos, F., Garcia-Ortiz, H., Rzhetskaya, M., Orozco, L., Raff, J. A., Hayes, M. G., & Bolnick, D. A.
- Affiliations
- University of California, Davis (US)
- Department of Anthropology, The University of Texas at Austin, Austin, TX 78712;
- Florida Museum of Natural History (US)
- University of Florida (US)
- Research on healthcare performance (FR)
- National Institute of Genomic Medicine (MX)
- National Institute of Genomic Medicine, Delegación Tlalpan, 14610 México;
- Northwestern University (US)
- University of Kansas (US)
- University of Connecticut (US)
- Corresponding author
- Reynolds, Austin W.
- ORCID
- Venue
- Proceedings of the National Academy of Sciences
- Publisher
- National Academy of Sciences
- Published
- 2019-04-15
- Volume
- 116
- Issue
- 19
- Pages
- 9312-9317
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- PMC
- PMC6511053
- OpenAlex
- W2939884405
- Cited by
- 67
- References
- 47
- Citations by year
- 2026: 2 · 2025: 8 · 2024: 5 · 2023: 7 · 2022: 11 · 2021: 30 · 2020: 2 · 2019: 1 · 2018: 1
- FWCI
- 6.63
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Proceedings of the National Academy of Sciences (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Science Foundation (1412501, 1408876)
- Wenner-Gren Foundation
- Texas Higher Education Coordinating Board
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- natural selection, human adaptation, cold adaptation, high latitudes, pathogen adaptation, population divergence, genome-wide selection signatures, Alaska, southeastern United States, central Mexico
- MeSH terms
- Genetics, Population, Haplotypes, Humans, Indians, North American, Selection, Genetic, Genome, Human, Polymorphism, Single Nucleotide, Genomics
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