Strong correlation between cross‐amplification success and genetic distance across all members of ‘True Salamanders’ (Amphibia: Salamandridae) revealed by Salamandra salamandra‐specific microsatellite loci

Abstract

The unpredictable and low cross-amplification success of microsatellite loci tested for congeneric amphibian species has mainly been explained by the size and complexity of amphibian genomes, but also by taxonomy that is inconsistent with phylogenetic relationships among taxa. Here, we tested whether the cross-amplification success of nine new and 11 published microsatellite loci cloned for an amphibian source species, the fire salamander (Salamandra salamandra), correlated with the genetic distance across all members of True Salamanders (genera Chioglossa, Lyciasalamandra, Mertensiella and Salamandra that form a monophyletic clade within the family of Salamandridae) serving as target species. Cross-amplification success varied strongly among the species and showed a highly significant negative relationship with genetic distance and amplification success. Even though lineages of S. salamandra and Lyciasalamndra have separated more than 30 Ma, a within genus amplification success rate of 65% was achieved for species of Lyciasalamandra thus demonstrating that an efficient cross-species amplification of microsatellite loci in amphibians is feasible even across large evolutionary distances. A decrease in genome size, on the other hand, paralleled also a decrease in amplified loci and therefore contradicted previous results and expectations that amplification success should increase with a decrease in genome size. However, in line with other studies, our comprehensive dataset clearly shows that cross-amplification success of microsatellite loci is well explained by phylogenetic divergence between species. As taxonomic classifications on the species and genus level do not necessarily mirror phylogenetic divergence between species, the pure belonging of species to the same taxonomic units (i.e. species or genus) might be less useful to predict cross-amplification success of microsatellite loci between such species.

Cross-species testing and utility of microsatellite loci in Indirana frogs

“…[19]). Our results from the Indirana genus conform to these general patterns, and the observed cross-species amplification success rate of 11.3-29.0 % (mean = 21.2 %) is comparable to the within-genus amplification success rate of approximately 21 % reported for Ranid frogs [20].…”

Isolation and Characterization of Cross-Amplification Microsatellite Panels for Species of Procapra (Bovidae; Antilopinae)

“…Sequence conservation of the flanking regions of microsatellite loci allowed primer pairs designed for one species to be shared with closely related taxa [49,50]. Among the Bovidae species, cross-species amplification of microsatellite primer pairs of Bos taurus showed 30 percent success rate in Capra hircus [51] and 40 percent in Ovis aries [49].…”

Genetic history of salmonid fishes of the genus Oncorhynchus

“…Studies in amphibians showed that the success of interspecific amplification was greatly variable, correlating with genetic distances between species. Moreover, it was phylogenetic divergence rather than the taxonomic position of the species that was the main criterion of successful interspecific amplification [78]. The review of the population structure of salmonids will continue and will also be focused on undergraduate and gradu ate students of different specialities.…”