A weakly structured stem for our origins in Africa

Despite broad agreement that Homo sapiens originated in Africa, considerable uncertainty surrounds specific models of divergence and migration across the continent. Progress is hampered by a shortage of fossil and genomic data, as well as variability in previous estimates of divergence times. I will give an overview of popular models for human origins and then discuss how newly sequenced whole genomes from Khoe-San individuals in southern Africa help test different hypotheses. In our research, we infer a reticulated African population history in which present-day population structure dates back to Marine Isotope Stage 5. The earliest population divergence among contemporary populations occurred 120,000 to 135,000 years ago and was preceded by links between two or more weakly differentiated ancestral Homo populations connected by gene flow over hundreds of thousands of years. Such “weakly structured stem” models explain patterns of polymorphism that had previously been attributed to contributions from archaic hominins in Africa. In contrast to models with archaic introgression, we predict that fossil remains from coexisting ancestral populations should be genetically and morphologically similar. I emphasize how “model misspecification” explains the variation in previous estimates of divergence times, and argue that studying a range of models is key to making robust inferences about deep history.