Biotools: an R function to predict spatial gene diversity via an individual-based approach

Abstract

The gene diversity or expected heterozygosity (H_E) is based on the allele frequency and is often used as a measure of genetic variability of populations. Knowing the pattern of spatial distribution of H_E can be useful for determining strategies of conservation and sampling of collections of individuals. In addition, it can allow one to detect genetic boundaries in a landscape. We adapted a Wombling method based on assignment tests in a circular moving window extensively sampled over the study area in order to estimate H_E at points of a prediction grid. The function sHe(), package biotools, is an easy-to-use and flexible implementation in R language that accepts as input geographical and genotyping data. The package biotools is distribution-free under the GPL-2/3 license and currently available from the Comprehensive R Archive Network (CRAN) at . The R platform and all R dependencies are similarly available from CRAN.