Data from: Single nucleotide polymorphisms reveal genetic structuring of the Carpathian newt and provide evidence of interspecific gene flow in the nuclear genome

Genetic variation within species is commonly structured in a hierarchical
manner which may result from superimposition of processes acting at
different spatial and temporal scales. In organisms of limited dispersal
ability, signatures of past subdivision are detectable for a long time.
Studies of contemporary genetic structure in such taxa inform about the
history of isolation, range changes and local admixture resulting from
geographically restricted hybridization with related species. Here we use
a set of 139 transcriptome-derived, unlinked nuclear single nucleotide
polymorphisms (SNP) to assess the genetic structure of the Carpathian newt
(Lissotriton montandoni, Lm) and introgression from its congener, the
smooth newt (L. vulgaris, Lv). Two substantially differentiated groups of
Lm populations likely originated from separate refugia, both located in
the Eastern Carpathians. The colonization of the present range in
north-western and south-western directions was accompanied by a modest
loss of variation; admixture between the two groups has occurred in the
middle of the Eastern Carpathians. Local, apparently recent introgression
of Lv alleles into several Lm populations was detected, demonstrating
increased power for admixture detection in comparison to a previous study
based on a limited number of microsatellite markers. The level of
introgression was higher in Lm populations classified as admixed than in
syntopic populations. We discuss the possible causes and propose further
tests to distinguish between alternatives. Several outlier loci were
identified in tests of interspecific differentiation, suggesting genomic
heterogeneity of gene flow between species.