Variogram Analysis of the Spatial Genetic Structure of Continuous Populations Using Multilocus Microsatellite Data

Abstract

A geostatistical perspective on spatial genetic structure may explain methodological issues of quantifying spatial genetic structure and suggest new approaches to addressing them. We use a variogram approach to (i) derive a spatial partitioning of molecular variance, gene diversity, and genotypic diversity for microsatellite data under the infinite allele model (IAM) and the stepwise mutation model (SMM), (ii) develop a weighting of sampling units to reflect ploidy levels or multiple sampling of genets, and (iii) show how variograms summarize the spatial genetic structure within a population under isolation-by-distance. The methods are illustrated with data from a population of the epiphytic lichen Lobaria pulmonaria, using six microsatellite markers. Variogram-based analysis not only avoids bias due to the underestimation of population variance in the presence of spatial autocorrelation, but also provides estimates of population genetic diversity and the degree and extent of spatial genetic structure accounting for autocorrelation.

Optimal sample sizes and allelic diversity in studies of the genetic variability of mycobiont and photobiont populations

“…For instance, the analysis of fine-scale spatial genetic patterns requires particularly large sample sizes at the population level (Wagner et al 2005;Werth et al 2006). If the aim of a study is to resolve the fine-scale probability of clonal identity (e.g., among branches of a tree), or fine-scale gene diversity, then the sample size recommended above might be on the lower end.…”

Population genetics of lichen-forming fungi – a review

“…Using variograms, my co-workers and I found significant spatial autocorrelation in genotype diversity and gene diversity of L. pulmonaria (Wagner et al 2005, Werth et al 2006b). Interestingly, the spatial extent of clonal structure differed between forest stands that had been subjected to different types of disturbances (Werth et al 2006b).…”

Propagule size is not a good predictor for regional population subdivision or fine-scale spatial structure in lichenized fungi

“…For the purpose of identifying isolation by distance in each species, we calculated spatial autocorrelation of genotype diversity following Wagner et al (2005) and Werth et al (2006b). Moreover, we tested for a correlation between Roger's genetic distance and Euclidean geographic distance using Mantel tests in R based on 9999 permutations.…”