Stairway Plot 2: demographic history inference with folded SNP frequency spectra
Xiaoming Liu, Yun‐Xin Fu
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.
Topics & Concepts
BiologyInferenceGenomicsSNPAllele frequencyPlot (graphics)Computational biologyPopulationNonparametric statisticsGeneticsSingle-nucleotide polymorphismEvolutionary biologyStatisticsGenomeComputer scienceMathematicsAlleleArtificial intelligenceGenotypeGeneSociologyDemographyGenomics and Phylogenetic StudiesGenetic diversity and population structureGenetic and phenotypic traits in livestock