Abstract

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

The gene diversity or expected heterozygosity (HE) 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 HE 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 HE 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 http://CRAN.R-project.org/package=biotools. The R platform and all R dependencies are similarly available from CRAN.

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