Differential natural selection of human zinc transporter genes between african and non-African populations.
Open accessAbstract
Zinc transporters play important roles in all eukaryotes by maintaining the rational zinc concentration in cells. However, the diversity of zinc transporter genes (ZTGs) remains poorly studied. Here, we investigated the genetic diversity of 24 human ZTGs based on the 1000 Genomes data. Some ZTGs show small population differences, such as SLC30A6 with a weighted-average FST (WA-FST = 0.015), while other ZTGs exhibit considerably large population differences, such as SLC30A9 (WA-FST = 0.284). Overall, ZTGs harbor many more highly population-differentiated variants compared with random genes. Intriguingly, we found that SLC30A9 was underlying natural selection in both East Asians (EAS) and Africans (AFR) but in different directions. Notably, a non-synonymous variant (rs1047626) in SLC30A9 is almost fixed with 96.4% A in EAS and 92% G in AFR, respectively. Consequently, there are two different functional haplotypes exhibiting dominant abundance in AFR and EAS, respectively. Furthermore, a strong correlation was observed between the haplotype frequencies of SLC30A9 and distributions of zinc contents in soils or crops. We speculate that the genetic differentiation of ZTGs could directly contribute to population heterogeneity in zinc transporting capabilities and local adaptations of human populations in regard to the local zinc state or diets, which have both evolutionary and medical implications.
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It is not obvious how the observed differential molecular phenotype for Met50Val can be translated into an adaptive phenotype at the organism level or might relate to environmental zinc.
“However, despite all the data we have compiled, it is not obvious how the observed differential molecular phenotype for the Met50Val substitution can be translated into an adaptive phenotype at the organism level or might relate to environmental zinc [13].”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [13]
The Discussion (page not available) identifies a variant at the 50th amino acid of SLC30A9 and explicitly speculates that it affects zinc transport and that local zinc concentrations influenced selection. This supports treating the environmental-zinc link as uncertain, but the paper does not report an observed molecular phenotype for Met50Val or assess how it translates into an organism-level adaptive phenotype. (LLM, conf=0.78)
Experimental — accuracy not yet measuredPrevious studies detected strong signatures of positive selection in the SLC30A9 region.
“The motivation for this study was the previous detection of strong signatures of positive selection in the SLC30A9 region [13,14,16,17,20,25].”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as [13]
Contrasting signals of positive selection between two major haplotypes in Africa and East Asia were confirmed.
“In accordance with Zhang et al. (2015) [13], we confirmed contrasting signals of positive selection between two major haplotypes in Africa and East Asia, the latter also being present at intermediate-high frequencies in South Asia, Europe, and America.”
From Human genetic adaptation related to cellular zinc homeostasis (2023) · cites this paper as Zhang et al. (2015) [13]
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Human genetic adaptation related to cellular zinc homeostasis
Roca-Umbert, A., Garcia-Calleja, J., Vogel-González, M., Fierro-Villegas, A., Ill-Raga, G., Herrera-Fernández, V., Bosnjak, A., Muntané, G., Gutiérrez, E., Campelo, F., et al. (2023) · PLoS Genetics · doi:10.1371/journal.pgen.1010950 · Cited by 8 · see citing works
- Authors
- Zhang, C., Li, J., Tian, L., Lu, D., Yuan, K., Yuan, Y., & Xu, S.
- Affiliations
- Chinese Academy of Sciences (CN)
- Corresponding author
- Xu, Shuhua
- Venue
- Scientific Reports
- Published
- 2015-04-30
- Volume
- 5
- Issue
- 1
- Pages
- 9658-9658
- ISSN
- 2045-2322 (ISSN-L)
- PMC
- PMC5386188
- OpenAlex
- W1994997048
- Cited by
- 27
- References
- 61
- Citations by year
- 2026: 1 · 2025: 5 · 2024: 3 · 2023: 2 · 2022: 1 · 2021: 3 · 2019: 4 · 2018: 2 · 2017: 3 · 2016: 2 · 2015: 1
- FWCI
- 1.82
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Scientific Reports (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Greater South Information System
- Funders
- National Natural Science Foundation of China (31370505, 31171218, 91331204)
- Chinese Academy of Sciences (XDB13040100)
- Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences
- Directorate for Biological Sciences
- Youth Innovation Promotion Association
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Health Sciences › Nursing › Nutrition and Dietetics › Trace Elements in Health
- Keywords
- zinc transporters, natural selection, genetic differentiation, African populations, East Asian populations, non-synonymous variants, haplotype frequencies, local adaptation, human genetic variation
- MeSH terms
- Alleles, Carrier Proteins, Biological Evolution, Gene Frequency, Genetics, Population, Haplotypes, Humans, Nuclear Proteins, Selection, Genetic, Transcription Factors, Genetic Variation, Cell Cycle Proteins, Polymorphism, Single Nucleotide, Cation Transport Proteins, Black People, White People, Asian People
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