Like many carnivore species, European wildcats (Felis silvestris) have suffered severe anthropogenic population declines in the past, resulting in a strong population bottleneck in the beginning of the 20th century. In Germany, the species has managed to survive its near-extinction in small isolated areas and is currently recolonizing former habitats owing to legal protection and concerted conservation efforts. Here, we SNP genotyped and mtDNA sequenced 56 historical and 650 contemporary samples to assess the impact of massive persecution on genetic diversity, population structure and hybridization dynamics of wildcats. Spatiotemporal analyses suggest that the presumed postglacial differentiation between two genetically distinct metapopulations in Germany is in fact the result of the anthropogenic bottleneck followed by re-expansion from few secluded refugia. We found that, despite the bottleneck, populations experienced no severe genetic erosion, nor suffered from elevated inbreeding or showed signs of increased hybridization with domestic cats. Our findings have significant implications for current wildcat conservation strategies, as the data analyses show that the two presently recognized wildcat population clusters should be treated as a single conservation unit. Although current populations appear under no imminent threat from genetic factors, fostering connectivity through the implementation of forest corridors will facilitate the preservation of genetic diversity and promote long-term viability. The present study documents how museum collections can be used as essential resource for assessing long-term anthropogenic effects on natural populations, e.g., regarding population structure and the delineation of appropriate conservation units, potentially informing todays’ species conservation.

The SNP data was genotyped with microfluidic 96.96 Dynamic Arrays™ (Fluidigm Corp., South San Francisco, USA) using a panel of 96 SNP markers described in a previous study (von Thaden et al. 2020).

The SNP genotypes are provided in variant call format (.vcf). The dataset consists of genotypes for 175 museum and 650 contemporary wildcat samples.

Sample names include (separated by underscore):

1. Sample ID (as referred to in corresponding article)
2. Sample type (F1, skin; G1, dried tissue remains; FB1, footpad; K1, bone; NMK1, turbinal bone; Z1, tooth)
3. Genotyping replicate (coded with "r1" to "r7")