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Population genetic evidence for positive and purifying selection acting at the human IFN-γ locus in Africa

Abstract

Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a “star-like” genealogy of African-specific haplotypes carrying variants previously associated with infectious disease. We also inferred a deep time to coalescence of variation at IFN-γ (~ 0.8 million years ago) and ancient ages for common polymorphisms predating the evolution of modern humans. Taken together, these results are congruent with a model of positive selection on standing variation in African populations. Furthermore, we inferred that common variants in intron 3 of IFN-γ are the likely targets of selection. In addition, we observed a paucity of non-synonymous substitutions relative to synonymous changes in the exons of IFN-γ in African and non-African populations, suggestive of strong purifying selection. Therefore, we contend that positive and purifying selection have influenced levels of diversity in different regions of IFN-γ, implying that these distinct genic regions are, or have been, functionally important. Overall, this study provides additional insights into the evolutionary events that have contributed to the frequency and distribution of alleles having a role in human health and disease.

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Acknowledgements

We thank the Center for Computational Biology and Bioinformatics (CCBB) at Howard University for providing cluster computational resources for this project. This work was supported by the Start-up Funds of Howard University to M.C. Campbell.

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Campbell, M.C., Smith, L.T. & Harvey, J. Population genetic evidence for positive and purifying selection acting at the human IFN-γ locus in Africa. Genes Immun 20, 143–157 (2019). https://doi.org/10.1038/s41435-018-0016-1

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