St<scp>AMPP</scp>: an R package for calculation of genetic differentiation and structure of mixed‐ploidy level populations

Abstract

Statistical Analysis of Mixed-Ploidy Populations (StAMPP) is a freely available R package for calculation of population structure and differentiation based on single nucleotide polymorphism (SNP) genotype data from populations of any ploidy level, and/or mixed-ploidy levels. StAMPP provides an advance on previous similar software packages, due to an ability to calculate pairwise FST values along with confidence intervals, Nei's genetic distance and genomic relationship matrixes from data sets of mixed-ploidy level. The software code is designed to efficiently handle analysis of large genotypic data sets that are typically generated by high-throughput genotyping platforms. Population differentiation studies using StAMPP are broadly applicable to studies of molecular ecology and conservation genetics, as well as animal and plant breeding.