Distinct haplogroups with star-like diversification in the APOBEC3 regulatory region indicate ancient viral pandemics before and during the Out-of-Africa migration of modern humans

Abstract

Human anti-viral APOBEC3s are crucial components of the innate immune response, playing a key role in inhibiting viral replication and proliferation by inducing mutations in viral genomes. In this study, in a regulatory region of [~]16 kb in the APOBEC3 gene cluster on human chromosome 22, we identified three distinct haplogroups that are maintained at high frequencies in both African and non-African populations today. Despite the long persistence of these haplogroups, one of which is shared by archaic hominins, the nucleotide diversity within each haplogroup was unusually low in non-Africans. The simultaneous observations of low intra-haplogroup diversity and high inter-haplogroup divergence were incompatible with neutrality, as demonstrated by the genome-wide empirical distribution and coalescence-based simulation tests. In addition to the three shared haplogroups, an ancestral sequence group was identified exclusively in African populations. To explain these features and investigate the underlying evolutionary mechanisms, we performed forward simulations to model the joint effects of balancing selection and population bottlenecks. We demonstrated the operation of balancing selection over the past [~]1 million years, as well as a hitherto unexplored reduction in intra-haplogroup diversity. The only unexplainable observation was the low diversity within African haplogroup I, which is unaffected by the non-African-specific bottleneck. We hypothesized that an extra haplotype turnover within haplogroup I occurred prior to the Out-of-Africa dispersal of modern humans. Finally, we discussed the functional importance of the APOBEC3 regulatory region in terms of evolutionary conservation in Hominidae, a target of natural selection in modern humans, and its relevance in GTEx eQTL. Significance statementThis study provides new insights into the joint effects of population bottlenecks and balancing selection on genetic diversity within haplogroups. First, we reveal how balancing selection interacts with demographic history to shape intra-haplogroup diversity, a previously unexplored aspect. Second, our findings are generalizable, as illustrated by the ABO locus--an established example of balancing selection--where low within-haplogroup diversity and high between-haplogroup divergence are also observed in non-African populations. Third, the involvement of balancing selection in a highly conserved regulatory region suggests functional significance in modulating the expression of all seven APOBEC3 genes. While further validation is needed, our findings underscore the evolutionary and functional importance of this region in human innate immunity.