Stairway Plot 2: demographic history inference with folded SNP frequency spectra

Abstract

Inferring the demographic histories of populations has wide applications in population, ecological, and conservation genomics. We present Stairway Plot 2, a cross-platform program package for this task using SNP frequency spectra. It is based on a nonparametric method with the capability of handling folded SNP frequency spectra (that is, when the ancestral alleles of the SNPs are unknown) of thousands of samples produced with genotyping-by-sequencing technologies; therefore, it is particularly suitable for nonmodel organisms.