Functional characterization of the Met50Val substitution in SLC30A9 as a novel case of adaptive introgression in humans

The SLC30A9 gene encodes a ubiquitously expressed zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. Here, we first validated the extreme signatures of adaptation found in the SLC30A9 region using evolutionary statistics based on population differentiation, extended haplotype homozygosity, and an excess of derived alleles. We then inferred the allelic trajectories and selection coefficients of two putative adaptive variants and tried to functionally validate their potential systemic and molecular adaptive phenotypes. Our results provide evidence for directional selection operating in two contrasting haplotypes extremely frequent in Africa and East Asia, respectively, which are not only associated with differential SLC30A9 expression levels but differ in a methionine-to-valine substitution (Met50Val; rs1047626) in ZnT9, which was likely adaptively introgressed from archaic humans. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the overexpression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Furthermore, the overexpression of the ZnT9 50Val variant avoids zinc overload in the endoplasmic reticulum and mitochondria, with an impact on cell viability and zinc toxicity. Overall, our results show that the derived ZnT9 50Val variant, which is prevalent in East Asians and found at intermediate-high frequencies in other non-African populations, is associated with functional differences in zinc handling by the mitochondria and endoplasmic reticulum, key organelles involved in cell fate and metabolism. Given the essential role of zinc in glutamatergic neurotransmission, we speculate that archaic adaptation to excitotoxicity may have driven this selection event in modern humans, while also impacting prosocial behavior and susceptibility to neuropsychiatric disorders. ### Competing Interest Statement The authors have declared no competing interest.