Hybridisation between domestic and wild taxa can pose severe threats to wildlife conservation, and human-induced hybridisation, often linked to species' introductions and habitat degradation, may promote reproductive opportunities between species for which natural interbreeding would be highly unlikely. Using a biome-specific approach, we examine the effects of a suite of ecological drivers on the European wildcat's genetic integrity, while assessing the role played by protected areas in this process. We used genotype data from 1217 putative European wildcat samples from 13 European countries to assess the effects of landcover, disturbance and legal landscape protection on the European wildcat's genetic integrity across European biomes, through generalised linear models within a Bayesian framework. Overall, we found European wildcats to have genetic integrity levels above the wildcat-hybrid threshold (ca. 83%; threshold = 80%). However, Mediterranean and Temperate Insular biomes (i.e., Scotland) revealed lower levels, with 74% and 46% expected genetic integrity, respectively. We found that different drivers shape the level of genetic introgression across biomes, although forest integrity seems to be a common factor promoting European wildcat genetic integrity. Wildcat genetic integrity remains high, regardless of landscape legal protection, in biomes where populations appear to be healthy and show recent local range expansions. However, in biomes more susceptible to hybridisation, even protected areas show limited effectiveness in mitigating this threat. In the face of the detected patterns, we recommend that species conservation and management plans should be biome- and landscape-context-specific to ensure effective wildcat conservation, especially in the Mediterranean and Temperate Insular biomes.

Abstract Aim Connectivity conservation is ideally based on empirical information on how landscape heterogeneity influences species‐specific movement and gene flow. Here, we present the first large‐scale evaluation of landscape impacts on genetic connectivity in the European wildcat (Felis silvestris), a flagship and umbrella species for connectivity conservation across Europe. Location The study was carried out in the core area of the distributional range of wildcats in Germany, covering about 186,000 km2 of a densely populated and highly fragmented landscape. Methods We used data of 975 wildcats genotyped at 14 microsatellites and an individual‐based landscape genetic framework to assess the importance of twelve landscape variables for explaining observed genetic connectivity. For this, we optimized landscape resistance surfaces for all variables and compared their relative impacts using multiple regression on distance matrices and commonality analysis. Results Genetic connectivity was best explained by a synergistic combination of six landscape variables and isolation by distance. Of these variables, road density had by far the strongest individual impact followed by synergistic effects of agricultural lands and settlements. Subsequent analyses involving different road types revealed that the strong effect of road density was largely due to state roads, while highways and federal roads had a much smaller, and county roads only a negligible impact. Main conclusions Our results highlight that landscape‐wide genetic connectivity in wildcats across Germany is strongly shaped by the density of roads and in particular state roads, with higher densities providing larger resistance to successful dispersal. These findings have important implications for conservation planning, as measures to mitigate fragmentation effects of roads (e.g., over‐ or underpasses) often focus on large, federally managed transportation infrastructures. While these major roads exert local barrier effects, other road types can be more influential on overall connectivity, as they are more abundant and more widespread across the landscape.

Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat ( Felis silvestris ) has been shown to hybridise with domestic cats ( Felis catus ). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.

The genomic era has led to an unprecedented increase in the availability of genome-wide data for a broad range of taxa. Wildlife management strives to make use of these vast resources to enable refined genetic assessments that enhance biodiversity conservation. However, as new genomic platforms emerge, problems remain in adapting the usually complex approaches for genotyping of noninvasively collected wildlife samples. Here, we provide practical guidelines for the standardized development of reduced single nucleotide polymorphism (SNP) panels applicable for microfluidic genotyping of degraded DNA samples, such as faeces or hairs. We demonstrate how microfluidic SNP panels can be optimized to efficiently monitor European wildcat (Felis silvestris S.) populations. We show how panels can be set up in a modular fashion to accommodate informative markers for relevant population genetics questions, such as individual identification, hybridization assessment and the detection of population structure. We discuss various aspects regarding the implementation of reduced SNP panels and provide a framework that will allow both molecular ecologists and practitioners to help bridge the gap between genomics and applied wildlife conservation.

Abstract Hybridization between wild species and their domestic congeners is considered a major threat for wildlife conservation. Genetic integrity of the European wildcat, for instance, is a concern as they are outnumbered by domestic cats by several orders of magnitude throughout its range. We genotyped 1,071 individual wildcat samples obtained from hair traps and roadkills collected across the highly fragmented forests of western Central Europe, in Germany and Luxembourg, to assess domestic cat introgression in wildcats in human‐dominated landscapes. Analyses using a panel of 75 autosomal SNPs suggested a low hybridization rate, with 3.5% of wildcat individuals being categorized as F1, F2, or backcrosses to either parental taxon. We report that results based on a set of SNPs were more consistent than on a set of 14 microsatellite markers, showed higher accuracy to detect hybrids and their class in simulation analyses, and were less affected by underlying population structure. Our results strongly suggest that very high hybridization rates previously reported for Central Europe may be partly due to inadequate choice of markers and/or sampling design. Our study documents that an adequately selected SNP panel for hybrid detection may be used as an alternative to commonly applied microsatellite markers, including studies relying on noninvasively collected samples. In addition, our finding of overall low hybridization rates in Central European wildcats provides an example of successful wildlife coexistence in human‐dominated, fragmented landscapes.

Noninvasively collected samples are a common source of DNA in wildlife genetic studies. Currently, single nucleotide polymorphism (SNP) genotyping using microfluidic arrays is emerging as an easy-to-use and cost-effective methodology. Here we assessed the performance of microfluidic SNP arrays in genotyping noninvasive samples from grey wolves, European wildcats and brown bears, and we compared results with traditional microsatellite genotyping. We successfully SNP-genotyped 87%, 80% and 97% of the wolf, cat and bear samples, respectively. Genotype recovery was higher based on SNPs, while both marker types identified the same individuals and provided almost identical estimates of pairwise differentiation. We found that samples for which all SNP loci were scored had no disagreements across the three replicates (except one locus in a wolf sample). Thus, we argue that call rate (amplification success) can be used as a proxy for genotype quality, allowing the reduction of replication effort when call rate is high. Furthermore, we used cycle threshold values of real-time PCR to guide the choice of protocols for SNP amplification. Finally, we provide general guidelines for successful SNP genotyping of degraded DNA using microfluidic technology.

After persecution and a long period of extinction in parts of central Europe, the European wildcat is currently increasing its range, also to areas deemed unsuitable for this species. This range expansion facilitates close contact with domestic cats, which can reach high population densities even in protected areas. We provide unambiguous evidence that the European wildcat is present in the Bavarian Forest National Park. We assessed the frequency of domestic cat occurrence, and analyzed the distributions of the two felid subspecies with regard to residential areas, forested habitat, elevation and protected areas, and analyzed their spatial overlap. Camera traps installed in the national park detected six putative wildcats in 2008–2015 at elevations between 800 and 1100 m a.s.l. Genetic analysis of material obtained from hair traps with valerian‐treated lure sticks confirmed the presence of three wildcat individuals in early 2015. The number of wildcat events detected increased slightly in recent years and wildcats were detected closer to shrub cover and the forest edge. Of the domestic cat events, 90% were within 1.1 km of residential areas, but some moved up to nearly 3 km into the national park. Ranges of wildcats and domestic cats broadly overlapped. All but one camera trap that recorded wildcats also recorded domestic cats, and some camera traps recorded domestic cats but no wildcats. Domestic cats were the fifth most often detected mammal species in the protected area. To avoid a negative impact of domestic cats on wildcats through hybridization, which might already occur, and considering the ecological impact of predation by domestic cats, we recommend a buffer zone of 1 km surrounding the national park, where domestic cats should not be allowed outdoors.

The European wildcat Felis silvestris silvestris is one of the most endangered mammals in Poland. In 1954, when the Tatra National Park (TNP) was established in the highest part of the Polish Carpathians, the wildcat was considered a rare species but nevertheless present in this region. However, its occurrence was never properly recorded there. The aim of this study was to verify whether wildcats occur in the TNP using genetic methods to distinguish wildcats from domestic cats F. s. catus. Between March and May 2015, hair samples were collected from 40 lure sticks treated with valerian, a cat attractant, in a region of the park with presumed high habitat suitability for wildcats. Neither wildcats nor hybrids with domestic cats were identified using control region haplotype sequencing and analysis of different nuclear markers. However, thirteen samples indicating the presence of the domestic cat in the protected area were collected. The Bayesian clustering analyses of microsatellite and SNP genotypes revealed no evidence for any admixture with wildcats. While our study cannot prove the absence of wildcats in the study area, it strongly suggests that wildcats are at least very rare in the region and a continued rigorous monitoring is recommended.

The European wildcat, Felis silvestris silvestris, serves as a prominent target species for the reconnection of central European forest habitats. Monitoring of this species, however, appears difficult due to its elusive behaviour and the ease of confusion with domestic cats. Recently, evidence for multiple wildcat occurrences outside its known distribution has accumulated in several areas across Central Europe, questioning the validity of available distribution data for this species. Our aim was to assess the fine-scale distribution and genetic status of the wildcat in its central European distribution range. We compiled and analysed genetic samples from roadkills and hundreds of recent hair-trapping surveys and applied phylogenetic and genetic clustering methods to discriminate wild and domestic cats and identify population subdivision. 2220 individuals were confirmed as either wildcat (n = 1792) or domestic cat (n = 342), and the remaining 86 (3.9 %) were identified as hybrids between the two. Remarkably, genetic distinction of domestic cats, wildcats and their hybrids was only possible when taking into account the presence of two highly distinct genetic lineages of wildcats, with a suture zone in central Germany. 44 % of the individual wildcats where sampled outside the previously published distribution. Our analyses confirm a relatively continuous spatial presence of wildcats across large parts of the study area in contrast to previous analyses indicating a highly fragmented distribution. Our results suggest that wildcat conservation and management should take advantage of the higher than previously assumed dispersal potential of wildcats, which may use wildlife corridors very efficiently.