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Dispersal is a key process for the maintenance of intraspecific genetic diversity by ensuring gene flow within and between populations. Despite the ongoing expansion of large carnivores in Europe, lynx populations remain fragmented, isolated, and threatened by inbreeding and loss of genetic diversity. In the course of large carnivore monitoring in the Czech Republic, several biological samples of Eurasian lynx were collected outside the permanent occurrence of this species. Using microsatellite genotyping we identified these as four dispersing lynx males and applied multiple methods (Bayesian clustering in STRUCTURE, Principal Component Analysis (PCA), frequency-based method in GENECLASS2, and machine-learning framework in assignPOP) to assign them to possible source populations. For this we used genotypes from five European lynx populations: the Bohemian-Bavarian-Austrian (N = 36), Carpathian (N = 43), Scandinavian (N = 20), Baltic (N = 15), and Harz (N = 23) population. All four dispersers were successfully assigned to different source populations within Europe and each was recorded at a distance of more than 98 km from the edge of the distribution of the source population identified. Such movements are among the longest described for lynx in Central Europe to this point. The findings indicate the ability of lynx males to disperse in human-dominated landscape thus facilitation of these movements via creation and/or protection of potential migratory corridors together with protection of dispersing individuals should be of high importance in conservation of this iconic predator in Central Europe.

Large carnivores have made a successful comeback across human-dominated landscapes in Central Europe. The Eurasian lynx, for instance, has been actively reintroduced in different regions. Genetic diversity is quickly eroding in these isolated, small populations, questioning the long-term success of lynx reintroductions. To track population development and genetic diversity in a reintroduced lynx population, we used microsatellite analysis and mtDNA haplotyping based on 379 samples collected during the initial 15 year period of lynx reintroduction in the Harz mountains National Park, Germany. The Harz lynx population shows higher genetic diversity relative to other lynx reintroductions, due to initial cross-breeding of divergent captive source lineages and a comparably high founder size. While the population shows significant population growth and spread into adjacent regions, genetic diversity is continiously declining. Expected heterozygosity values dropped from 0.63 after reintroduction (2006/2007) to 0.55 within a 10 year period. Despite this, the Harz lynx population is currently a viable component to an envisioned lynx metapopulation spanning across Central Europe. The ongoing genetic erosion in the Harz population along with a lack of geneflow from adjacent populations indicates that such connectivity is urgently needed to ensure long-term population persistence.

The development and use of cost-effective and appropriate survey methods to assess species distribution and to monitor range expansion and contraction of wild populations is crucial due to the limited financial resources for conservation. Of particular importance, yet little studied, is the ability to collect information before a wild population is well established, i.e. at the early stages of recolonisation. During 2018 and 2019, we used camera traps, audio recorders, and scat detection dogs simultaneously to investigate composition, detection probability, and territorial extent of a pack of wolves in the Swiss Alps. We compared the efficacy of these survey methods by assessing sampling effort, data obtained, and costs. We show that, under the presented setup, camera traps and scat detection dogs substantially outperformed audio recorders in detecting wolves, representing the packs’ territorial extent, and revealing the number of adult wolves. The detection dogs did not detect pups but, unlike the other methods, allowed the identification of single individuals. The use of four camera traps during 13 weeks, a 24-km-long transect walked with the detection dog, or the use of one audio recorder during 148 weeks were necessary to obtain a comparable wolf detection probability. Our results show that no single method was able to return all information that we hoped to collect. Comprehensive and cost-effective information was best obtained by combining data from camera traps and detection dogs. We suggest both methods to be simultaneously used to successfully investigate wolf recolonisation into historical range.

Following severe population decline and local extinction due to massive habitat destruction and persecution, wildcats have recently reappeared in several parts of Germany’s low mountain region. It remains unknown how this reemergence occurred, specifically if local populations have been overlooked at low densities or if the species has successfully spread across the highly fragmented anthropogenic landscape. In the central German Rhön Mountains, for instance, wildcats were believed to be extinct during most of the twentieth century, however, the species was recently detected and subsequent genetic monitoring found the presence of a sizeable population. In this study, we used microsatellite and SNP genotypes from 146 wildcat individuals from 2008 to 2017 across a ~ 15,000 km2area in the central German low mountain region to understand the population re-establishment of wildcats in the region. Bayesian clustering and subsequent analyses revealed that animals in the Rhön Mountains appear to be a mix from the two adjacent populations in the North and South of the area, suggesting a recent range expansion from two different directions. Both populations meet in the Rhön Biosphere Reserve, leading to an admixture of the northern, autochthonous, and the southern reintroduced wildcat population. While we cannot completely exclude the possibility of undetected population persistence, the high genetic homogeneity in the central German wildcat population and the lack of any signatures of past population decline in the Rhön favor a scenario of natural expansion. Our findings thus suggest that wildcats are well capable of rapid range expansion across richly structured landscape mosaics consisting of open land, settlements, and forest patches and document the potential of massive non-invasive genetic sampling when aiming to reconstruct the complex population and range dynamics of wildlife.

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 non-invasively 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.

As Eurasian lynx (Lynx lynx) show signs of population recovery in parts of Central Europe, sound monitoring strategies are required to study population expansion, connectivity and genetic diversity. While non-invasive DNA sampling strategies could serve this task, genetic samples of lynx are generally hard to locate. To test the suitability of dog-based sampling we searched scat samples of lynx in the Bavarian Forest National Park, Germany, with two trained detection dog teams. In 44 grid cells of 2 × 2 km, dog teams covered 440 km of predetermined forest road and hiking trail transects during the four week survey. A total of 169 collected samples resulted in 52 genetically confirmed lynx detections, of which 26 were assigned to 11 individuals. Using a single-season site occupancy model we found a detection probability of 0.13/km (SD = 0.02), with 10 km of dog search per grid cell required to get a 70 % probability to detect lynx presence. Our results show that detection dogs are an appropriate tool for systematic genetic lynx monitoring. We argue that detection dog-assisted genetic monitoring may supplement monitoring strategies based on conventional camera trapping, especially when aiming to monitor genetic diversity and population connectivity.

Here we present an approach to establish species-specific genetic markers for sex identification suitable for non-invasive samples. Such markers are not yet available for the endangered common hamster (Cricetus cricetus) because of the lack of genomic resources. Using Y chromosome conserved anchored tagged sequences (YCATS) exonic primers, we obtained Y-chromosomal sequences from hamsters and sympatric rodent species. From this, we designed hamster-specific primers targeting two short Y-chromosomal intron fragments and included them in microsatellite multiplex reactions, using autosomal loci also as amplification controls. The method yielded highly consistent results. The approach can be easily applied to development of sex markers in species for which there are no genome sequences available and thus aid conservation genetics efforts.

The ultimate strategy to prevent species extinction is captive breeding followed by reintroduction of individuals into the wild. Unfortunately, overall success of reintroductions is poor and in most cases conservation breeding is applied for species where individual numbers, population numbers and genetic diversity is strongly reduced. In addition, reintroductions inevitably result in small populations with poor genetic status. Systematic demographic and genetic monitoring is needed to optimize conservation actions. Here we show how genetic monitoring was useful and informative in a reintroduction project for the highly endangered Common hamster (Cricetus cricetus) in the Netherlands and Belgium. Using well defined breeding lines of original relict populations combined with a systematic reintroduction scheme including consecutive supplementations made it possible to infer success of reintroduction, supplementation and following admixture of populations. An initial loss of genetic diversity could be detected in some of the reintroduced populations, but it could be shown that due to following supplementation of populations, genetic diversity and also effective population size in the wild stabilized or even increased. Multivariate (DAPC) and Bayesian inference (STRUCTURE) revealed admixture of supplemented individuals with wild-born individuals. Although population size estimates differed strongly between populations, a link between census size, breeding lines, effective population size and genetic diversity could not be proven. This study highlights that genetic monitoring is not only descriptive but also reveals detailed information on reintroduction success, admixture and population development. We recommend that genetic monitoring should be a basic element of reintroductions and should be used to optimize reintroduction attempts.

The Common hamster (Cricetus cricetus) faced massive population declines throughout its western range margin. In France, relict populations remained in the Alsace region. By comparing allelic diversity using microsatellite analysis over a time span of 12 years we investigated if this population decline led to genetic erosion in a French relict population of the species. Genetic diversity was moderate but comparable to other populations from Western Europe. Interestingly, no decline of allelic variation was revealed between 1999 and 2012 in the study region (expected heterozygosity = 0.51 in 1999 and 0.5 in 2012, respectively), suggesting a sufficiently high effective population size of ∼500 (179–956 SD). While several alleles were lost in a captive breed maintained for restocking purposes in the region, expected heterozygosity was comparably high (=0.5). Our results show that genetic diversity has been effectively maintained in a relict population of French Common hamsters despite of massive range loss. We recommend the maintenance of intense in situ conservation effort, along with regular monitoring of genetic diversity and effective population size.

The Balkans are one of the last large refugia for brown bear ( Ursus arctos ) populations in Europe, and Bulgaria, in particular, contains relatively large areas of suitable brown bear habitat and a potential population of more than 600 individuals. Despite this, the majority of brown bear research remains focused on bear populations in Central and Western Europe. We provide the first assessment of genetic population structure of brown bears in Bulgaria by analysing tissue samples ( n = 16) as well as samples collected with noninvasive genetic methods, including hair and faecal samples ( n = 189 and n = 163, respectively). Sequence analysis of a 248 base pair fragment of the mitochondrial control region showed that two highly divergent mitochondrial European brown bear lineages form a contact zone in central Bulgaria. Furthermore, the analysis of 13 polymorphic microsatellite markers identified 136 individuals and found substantial genetic variability ( H e = 0.74; N A = 8.9). The combination of both genetic markers revealed the presence of weak genetic substructure in the study area with considerable degrees of genetic admixture and the likely presence of migration corridors between the two subpopulation in the Rhodope Mountains and Stara Planina as evidenced from the genetic detection of two male long-distance dispersers. A detailed assessment from densely collected samples in the Rhodope Mountains resulted in a population size estimate of 315 (95% CI = 206–334) individuals, indicating that not all available habitat is presently occupied by bears in this region. Efficient management plans should focus on preserving connectivity of suitable habitats in order to maintain gene flow between the two Bulgarian brown bear subpopulations.

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. published

As sample quality and quantity is a crucial factor in non-invasive genetics, we focused on the improvement of sampling efficiency of glue hair traps. We invented an optimized hair trap with moveable parts which enhanced sampling of high-quality genetic material. With the aid of the optimized hair trap, we were able to remotely pluck a sufficient amount of hair bulbs from our study animal the common hamster (Cricetus cricetus) with a trapping success of 49.3% after one survey night. The number of collected hairs with bulbs ranged between 1 and 50, with an average of 20.7 ± 14.8. Subsequently, the use of the hair trap in combination with a simplified laboratory routine allowed us to amplify species-specific microsatellites with an amplification success of 96.2% and ADO of 4.6%. This optimized trap may find usage for species identification or could be used as an instrument for long-term genetic monitoring of mammal populations.

Facing the ongoing decline in garden dormice (Eliomys quercinus) in large parts of Europe, data about genetic diversity, weight, size, and parasite burden were collected from live individuals (n = 156) from Hesse and Rhineland-Palatinate, Germany. Blood was collected under Isoflurane-oxygen-anaesthesia from the anterior vena cava or jugular vein, respectively. Sex, weight, tibiotarsal and tail length of all animals were recorded. Genetic analysis (n = 64) using hair samples, viral examinations of oral, ocular and anal swabs (n = 156) and parasitological examination of faecal samples (n = 57) were performed. Genetic analysis of mitochondrial DNA revealed three haplotypes in the study area (WE4, WE4-3, WE5). Microsatellite analysis demonstrated a comparably high genetic diversity with 66 % overlap of alleles, a low genetic distance (DJost 5.6 %) and a low index of differentiation (FST = 0.02) between individuals from Hesse and Rhineland-Palatinate. All swab samples were negative for Borna disease virus. In 47 % of the faecal samples Entamoeba sp. cysts, Eimeria sp. oocysts, and eggs of trematodes, cestodes (Hymenolepis spp.) and nematodes (Capillaria spp., Strongylida) were detected. To our knowledge, this is the first report of inhalation anaesthesia, clinical examination, blood collection and assessment of Borna disease virus in living garden dormice.

International audience; Key messageWe forecasted the effects of climate change and forest conversion options on common forest bird species by employing nation-wide high-resolution models. The results give details on how, where, and for which species forest conversion can mitigate climate change effects.Context To mitigate effects of climate change on forests, alterations are required to convert forests into less vulnerable forest types. Coniferous forest that has been cultivated extensively outside its natural range has been identified as being more vulnerable to climate change effects than deciduous forest.Aims The aim is to evaluate the effect of climate change mitigation measures on biodiversity due to forest conversion.MethodsWe generated five forest scenarios for Germany in which we systematically replaced coniferous with deciduous forest types. We forecasted the effects of climate change and forest conversion options on 25 forest bird species by employing high-resolution models to predict their current and future ranges and population size.Results Our simulations and modeling approach clearly predicted that climate change has a stronger impact on populations compared to distribution areas of common forest bird species. Forest conversion was predicted to amplify (15 species) and to weaken (10 species) the predicted gains and losses of species’ population size due to climate change. Using the total bird population size to evaluate the mitigation effect of the different forest scenarios, forest conversion below an elevation of 500 m a.s.l. was predicted to mitigate climate change effects by 0.3 million breeding pairs (−10 %). The relatively weak mitigation effect was mainly due to few generalist species that inhabit coniferous forests in large abundances and did not profit from a conversion to deciduous forests. Conclusion The results of the study give details on how, where, and for which species forest conversion can mitigate the anticipated effects of climate change.

Estimates of genetic diversity and phylogenetic affiliation represent an important resource for biodiversity assessment and a valuable guide to conservation and management. We have found a new population (Jawor—JW) of the common hamster Cricetus cricetus in western Poland that is remote from the nearest populations by 235–300 km. With the objective of genetically characterizing of this population, we compared it with other populations from Poland and Germany by taking into account sequences of four mitochondrial DNA genes and variation at 10 microsatellite loci. The JW population exhibited low levels of genetic diversity and allelic and haplotype richness, which likely reflects its extreme isolation. This factor, coupled with inbreeding and genetic drift, are major threats to JW. A neighbor-joining tree based on mtDNA haplotypes shows that JW clusters among samples representing the Central subgroup that is known from central Germany but that has not yet been identified in Poland. Findings presented here improve our understanding of the spread and diversification of the common hamster. We offer the following hypotheses to explain the observed pattern of mtDNA haplotype distribution: JW could be a byproduct of postglacial migrations or back-migrations from eastern refugia to the western part of Europe, or/and be a result of population and habitat fragmentation. We recommend translocation of individuals as an effective management strategy, both at the level of Central phylogeographic group and at the species level, to overcome the negative consequences of inbreeding and geographical isolation of the JW population.