Abstract
In population or landscape genetics studies, an unbiased sampling scheme is essential for generating accurate results, but logistics may lead to deviations from the sample design. Such deviations may come in the form of sampling multiple life stages. Presently, it is largely unknown what effect sampling different life stages can have on population or landscape genetic inference, or how mixing life stages can affect the parameters being measured. Additionally, the removal of siblings from a data set is considered best-practice, but direct comparisons of inferences made with and without siblings are limited. In this study, we sampled embryos, larvae, and adult Ambystoma maculatum from five ponds in Missouri, and analyzed them at 15 microsatellite loci. We calculated allelic richness, heterozygosity and effective population sizes for each life stage at each pond and tested for genetic differentiation (FST and DC) and isolation-by-distance (IBD) among ponds. We tested for differences in each of these measures between life stages, and in a pooled population of all life stages. All calculations were done with and without sibling pairs to assess the effect of sibling removal. We also assessed the effect of reducing the number of microsatellites used to make inference. No statistically significant differences were found among ponds or life stages for any of the population genetic measures, but patterns of IBD differed among life stages. There was significant IBD when using adult samples, but tests using embryos, larvae, or a combination of the three life stages were not significant. We found that increasing the ratio of larval or embryo samples in the analysis of genetic distance weakened the IBD relationship, and when using DC, the IBD was no longer significant when larvae and embryos exceeded 60% of the population sample. Further, power to detect an IBD relationship was reduced when fewer microsatellites were used in the analysis.
Highlights
Many organisms have high fecundity, but experience extremely high mortality
Our literature search revealed that mixed tissues have been used in about one fifth of amphibian population genetic studies using microsatellites, despite the lack of knowledge concerning the effects that this may have on population or landscape genetic inferences
We found little evidence for adverse effects of including siblings or with mixing tissue samples collected from different life stages when assessing levels of allelic richness, heterozygosity, or effective population size
Summary
Many organisms have high fecundity, but experience extremely high mortality. Most amphibian, fish and insect species are characterized by Type III survivorship, in which a majority of young individuals will die before reaching sexual maturity, and the genetic characteristics of these life stages may differ from the few surviving adults due to the decrease in population size (Frankham 1996). Numerous studies have assessed the role of inbreeding and heterozygosity on individual fitness (e.g., Balloux et al 2004; Ficetola et al 2011; Harrison et al 2011; Slate et al 2004). Both of these population genetic attributes are relevant in species of conservation concern, which often exist in small or isolated populations. Given the interaction between selection pressures and genetic diversity, it is not unreasonable to believe that population genetic measures may differ depending on the age or life stage of the sampled cohort
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