Data from: Effects of sample size and full sibs on genetic diversity characterization: a case study of three syntopic Iberian pond-breeding amphibians

Accurate characterization of genetic diversity is essential for
understanding population demography, predicting future trends and
implementing efficient conservation policies. For that purpose, molecular
markers are routinely developed for nonmodel species, but key questions
regarding sampling design, such as calculation of minimum sample sizes or
the effect of relatives in the sample, are often neglected. We used
accumulation curves and sibship analyses to explore how these 2 factors
affect marker performance in the characterization of genetic diversity. We
illustrate this approach with the analysis of an empirical dataset
including newly optimized microsatellite sets for 3 Iberian amphibian
species: Hyla molleri, Bufo calamita, and Pelophylax perezi. We studied
17–21 populations per species (total n = 547, 652, and 516 individuals,
respectively), including a reference locality in which the effect of
sample size was explored using larger samples (77–96 individuals). As
expected, FIS and tests for Hardy–Weinberg equilibrium and linkage
disequilibrium were affected by the presence of full sibs, and most
initially inferred disequilibria were no longer statistically significant
when full siblings were removed from the sample. We estimated that to
obtain reliable estimates, the minimum sample size (potentially including
full sibs) was close to 20 for expected heterozygosity, and between 50 and
80 for allelic richness. Our pilot study based on a reference population
provided a rigorous assessment of marker properties and the effects of
sample size and presence of full sibs in the sample. These examples
illustrate the advantages of this approach to produce robust and reliable
results for downstream analyses.