Using Aspects of the Site Frequency Spectrum to Determine Demographic History in Ancient and Modern Populations

The site frequency spectrum characterizes the variation found within different studied populations, providing insight on past demographic history. Here, I describe two methods of studying demographic history that condition or transform the site frequency spectrum to provide greater understanding of demographic history. The doubly conditioned site frequency spectrum helps to highlight differences between admixture and ancient structure models, helping to confirm that Neanderthals did admix with the ancestors of non-African humans. Projection analysis compares a single test genome to a reference population and provides insight on the demographic relationship between the reference and test populations analyzed. This method has been applied in humans to better articulate human demographic history and demonstrate the utility of the method. It has also been applied to genomic data from ancient and modern horses, highlighting admixture between the Przewalski’s horse and domestic horses, as well as the relationship of several ancient horse genomes to present day horse populations