Past Climate and Cultural Impacts on African Human Genetic Diversity

Total genomic diversity in humans increases when populations are isolated from each other for extended periods. However, the role of past astronomically forced climate conditions in the generation of human diversity remains unresolved. Here, we employ an agent-based model with genetic inheritance, a representation of culture, and realistic climate conditions to simulate the genetic history of African hominin populations throughout the Pleistocene. Our simulations of human population density and DNA changes show the dominant effect of Milanković cycles on dispersal, population structure, and genomic diversity. Warm early Pleistocene climates supported a heterogeneous patchwork of genetically diverse subpopulations across Africa. However, with the onset of colder conditions and reduced food resources at ~900 thousand years ago, human populations disappeared everywhere except in southern and eastern Africa. The corresponding simulated rapid decline in nucleotide diversity during this time is consistent with archaeological and genomic evidence. Following this regime change, humans began adapting to harsher climatic conditions, leading to rapid population expansions across the continent during interglacials. Boosted further by the spread of cultural traits and facilitated by warm, wet climate corridors over the last 400 thousand years, eastern African hominin populations eventually dispersed into Eurasia, contributing to the emergence of new geographically isolated populations and distinct genomic lineages.