Genomic inference of a human super bottleneck in the Early Stone Age

The demographic history has been a foundation of human evolutionary studies for more than a century. In this study, we developed a novel method referred to as the fast infinitesimal time coalescent (FitCoal) process. This method allows the accurate calculation of the composite likelihood of a site frequency spectrum and provides the precise inference of recent and ancient demographic history. Genomic sequences of the 1000 Genomes Project and the Human Genome Diversity Project – Centre d’Etude du Polymorphisme Humain panel were analyzed. Results showed that all ten African populations had a population super bottleneck, a small effective size of approximately 1,280 breeding individuals between 813 and 930 thousand years ago, and a 20-fold rapid growth at the end of the bottleneck. The super bottleneck caused a loss of 65.85% in current human genetic diversity, but it may have separated our ancestors from other hominins. Further analysis confirmed the existence of the super bottleneck in all 40 non-African populations. Our results provide new insights into human evolution in the Early Stone Age.