Data from: Stronger transferability but lower variability in transcriptomic- than in anonymous microsatellites: evidence from Hylid frogs.

A simple way to quickly optimize microsatellites in non-model organisms is
to re-use loci available in closely related taxa; however, this approach
can be limited by the stochastic and low cross-amplification success
experienced in some groups (e.g. amphibians). An efficient alternative is
to develop loci from transcriptome sequences. Transcriptomic
microsatellites have been found to vary in their levels of cross-species
amplification and variability, but this has to date never been tested in
amphibians. Here, we compare the patterns of cross-amplification and
levels of polymorphism of 18 published anonymous microsatellites isolated
from genomic DNA versus 17 loci derived from a transcriptome, across nine
species of tree frogs (Hyla arborea and Hyla cinerea group). We
established a clear negative relationship between divergence time and
amplification success, which was much steeper for anonymous than
transcriptomic markers, with half-lives (time at which 50% of the markers
still amplify) of 1.1 and 37 My respectively. Transcriptomic markers are
significantly less polymorphic than anonymous loci, but remain variable
across diverged taxa. We conclude that the exploitation of amphibian
transcriptomes for developing microsatellites is an optimal approach for
multi-species surveys (e.g. analyses of hybrid zones, comparative linkage
mapping), while anonymous microsatellites may be more informative for
fine-scale analyses of intraspecific variation. Moreover, our results
confirm the pattern that microsatellite cross-amplification is greatly
variable among amphibians, and should be assessed independently within
target lineages. Finally, we provide a bank of microsatellites for
Palearctic tree frogs (so far only available for H. arborea), which will
be useful for conservation and evolutionary studies in this radiation.