Exploring Population Size Changes Using SNP Frequency Spectra

Inferring demographic history is an important task in population genetics. Many existing inference methods are based on pre-defined simplified population models, which are more suitable for hypothesis testing than for exploratory analysis. We developed a novel model-flexible method called stairway plot, which infers population size changes over time using SNP frequency spectra. This method is applicable for whole-genome sequences of hundreds of individuals. Using extensive simulation we demonstrated the usefulness of the method for inferring demographic history, especially recent population size changes. The method was applied to the whole genome sequence data of nine populations from the 1000 Genomes Project, and showed a pattern of human population fluctuations from 10 to 200 thousand years ago.