Data from: Genetic pollution of a threatened native crested newt species through hybridization with an invasive congener in the Netherlands

Genetic pollution of a native species through hybridization with an
invasive species poses an insidious conservation threat. To expose genetic
pollution, molecular methods employing multilocus data are required. We
present a case study of genetic pollution via hybridization of a native
crested newt species, Triturus cristatus, by the invasive T. carnifex on
the Veluwe in the Netherlands. We sequenced 50 nuclear markers by next
generation sequencing and one mitochondrial marker by Sanger sequencing
for four populations from the native range of both parent species and
eleven ponds on the Veluwe. We use three population genetic approaches
(HIest, BAPS and Structure) to determine the genetic composition of the
Veluwe newts based on all nuclear markers, a subset of 18 diagnostic
markers and the complementary 32 non-diagnostic markers, with and without
parental populations. BAPS underestimates genetic pollution, whereas
Structure is comparatively accurate compared to HIest, although
Structure’s relative advantage decreases with the diagnosticity of the
markers. Data simulation confirms these findings. Genetic composition of
the Veluwe ponds ranges from completely native, via different degrees of
genetic admixture, to completely invasive. The observed hybrid zone
appears to be bimodal, suggesting negative selection against hybrids. A
genetic footprint of the native species is present in invasive
populations, evidencing that the invasive locally replaced the native
species. Genetic pollution is currently confined to a small area, but the
possibility of further expansion cannot be excluded. Removal of genetic
pollution will not be easy. We emphasize the need for legal guidance to
manage genetic pollution.