Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping

in Amphibia-Reptilia
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Skin swabbing, a minimally invasive DNA sampling method recently developed on adult amphibians, was tested on larvae of fire salamanders (Salamandra salamandra). The quality and quantity of the sampled DNA was evaluated by (i) measuring DNA concentration in DNA extracts, (ii) sequencing part of the mtDNA cytochrome b gene (692 bp) and (iii) genotyping eight polymorphic nuclear microsatellite loci. The multiple-tubes approach was used for calculating allelic dropout (ADO) and false allele (FA) rates to evaluate the reliability of the genotypes. DNA extracts from tissue samples of road-killed individuals were included in the study as positive controls. Our results showed that skin swabs of fire salamander larvae can provide DNA in sufficient quantity and quality, as sequencing was successful and no allelic dropouts or false alleles were detected. This method, tested for the first time on amphibian larvae, has proven to be an efficient and reliable alternative to the controversial tail fin clipping procedure.

Skin swabbing of amphibian larvae yields sufficient DNA for efficient sequencing and reliable microsatellite genotyping

in Amphibia-Reptilia



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    Effects of the observer and the handling experience (number of individuals handled so far, for each observer independently) on the square-root transformed DNA yield (in ng) obtained from larval skin swabs (full dataset including samples eluted in 200 or 250 μl). Black and white circles represent samples collected by observer 1 and 2 respectively. Lines represent the linear model: yieldsqrt ∼ observer ∗ handling experience, fitted in R version 2.14.0 (R Development Core Team, 2011).

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