sGD: software for estimating spatially explicit indices of genetic diversity
Molecular Ecology Resources, (2011)DOI: 10.1111/j.1755-0998.2011.03035.x
Abstract
Anthropogenic landscape changes have greatly reduced the population size, range and migration rates of many terrestrial
species. The small local effective population size of remnant populations favours loss of genetic diversity leading to
reduced fitness and adaptive potential, and thus ultimately greater extinction risk. Accurately quantifying genetic diversity
is therefore crucial to assessing the viability of small populations. Diversity indices are typically calculated from the mul-
tilocus genotypes of all individuals sampled within discretely defined habitat patches or larger regional extents. Impor-
tantly, discrete population approaches do not capture the clinal nature of populations genetically isolated by distance or
landscape resistance. Here, we introduce spatial Genetic Diversity (sGD), a new spatially explicit tool to estimate genetic
diversity based on grouping individuals into potentially overlapping genetic neighbourhoods that match the population
structure, whether discrete or clinal. We compared the estimates and patterns of genetic diversity using patch or regional
sampling and sGD on both simulated and empirical populations. When the population did not meet the assumptions of
an island model, we found that patch and regional sampling generally overestimated local heterozygosity, inbreeding and
allelic diversity. Moreover, sGD revealed fine-scale spatial heterogeneity in genetic diversity that was not evident with
patch or regional sampling. These advantages should provide a more robust means to evaluate the potential for genetic fac-
tors to influence the viability of clinal populations and guide appropriate conservation plans.