Surveys on Baylisascaris procyonis in two of the three French wild raccoon populations

Human infection by Baylisascaris procyonis can result in larva migrans syndromes, which can cause severe neurological sequelae and fatal cases. The raccoon serves as the definitive host of the nematode, harboring adult worms in its intestine and excreting millions of eggs into the environment via its feces. Transmission to paratenic hosts (such as rodents, birds and rabbits) or to humans occurs by accidental ingestion of eggs. The occurrence of B. procyonis in wild raccoons has been reported in several Western European countries. In France, raccoons have currently established three separate and expanding populations as a result of at least three independent introductions. Until now the presence of B. procyonis in these French raccoon populations has not been investigated. Between 2011 and 2021, 300 raccoons were collected from both the south-western and north-eastern populations. The core parts of the south-western and north-eastern French raccoon populations were free of B. procyonis. However, three worms (molecularly confirmed) were detected in a young raccoon found at the edge of the north-eastern French raccoon population, close to the Belgian and Luxemburg borders. Population genetic structure analysis, genetic exclusion tests and factorial correspondence analysis all confirmed that the infected raccoon originated from the local genetic population, while the same three approaches showed that the worms were genetically distinct from the two nearest known populations in Germany and the Netherlands. The detection of an infected raccoon sampled east of the northeastern population raises strong questions about the routes of introduction of the roundworms. Further studies are required to test wild raccoons for the presence of B. procyonis in the area of the index case and further east towards the border with Germany.

eDNA-based monitoring of Batrachochytrium dendrobatidis and Batrachochytrium salamandrivorans with ddPCR in Luxembourg ponds: taking signals below the Limit of Detection (LOD) into account

BACKGROUND

Batrachochytrium dendrobatidis (Bd) and Batrachochytrium salamandrivorans (Bsal) are two pathogenic fungi that are a significant threat to amphibian communities worldwide. European populations are strongly impacted and the monitoring of the presence and spread of these pathogens is crucial for efficient decision-making in conservation management.

RESULTS

Here we proposed an environmental DNA (eDNA) monitoring of these two pathogenic agents through droplet digital PCR (ddPCR) based on water samples from 24 ponds in Luxembourg. In addition, amphibians were swabbed in eight of the targeted ponds in order to compare the two approaches at site-level detection. This study allowed the development of a new method taking below-Limit of Detection (LOD) results into account thanks to the statistical comparison of the frequencies of false positives in no template controls (NTC) and below-LOD results in technical replicates. In the eDNA-based approach, the use of this method led to an increase in Bd and Bsal detection of 28 and 50% respectively. In swabbing, this resulted in 8% more positive results for Bd. In some samples, the use of technical replicates allowed to recover above-LOD signals and increase Bd detection by 35 and 33% respectively for eDNA and swabbing, and Bsal detection by 25% for eDNA.

CONCLUSIONS

These results confirmed the usefulness of technical replicates to overcome high levels of stochasticity in very low concentration samples even for a highly sensitive technique such as ddPCR. In addition, it showed that below-LOD signals could be consistently recovered and the corresponding amplification events assigned either to positive or negative detection via the method developed here. This methodology might be particularly worth pursuing in pathogenic agents' detection as false negatives could have important adverse consequences. In total, 15 ponds were found positive for Bd and four for Bsal. This study reports the first record of Bsal in Luxembourg.

Quantifying uncertainty in inferences of landscape genetic resistance due to choice of individual-based genetic distance metric

Estimates of gene flow resulting from landscape resistance inferences frequently inform conservation management decision-making processes. Therefore, results must be robust across approaches and reflect real-world gene flow instead of methodological artefacts. Here, we tested the impact of 32 individual-based genetic distance metrics on the robustness and accuracy of landscape resistance modelling results. We analysed three empirical microsatellite datasets and 36 simulated datasets that varied in landscape resistance and genetic spatial autocorrelation. We used ResistanceGA to generate optimised multi-feature resistance surfaces for each of these datasets using 32 different genetic distance metrics. Results of the empirical dataset demonstrated that the choice of genetic distance metric can have strong impacts on inferred optimised resistance surfaces. Simulations showed accurate parametrisation of resistance surfaces across most genetic distance metrics only when a small number of environmental features was impacting gene flow. Landscape scenarios with many features impacting gene flow led to a generally poor recovery of true resistance surfaces. Simulation results also emphasise that choosing a genetic distance metric should not be based on marginal R2 -based model fit. Until more robust methods are available, resistance surfaces can be optimised with different genetic distance metrics and the convergence of results needs to be assessed via pairwise matrix correlations. Based on the results presented here, high correlation coefficients across different genetic distance categories likely indicate accurate inference of true landscape resistance. Most importantly, empirical results should be interpreted with great caution, especially when they appear counter-intuitive in light of the ecology of a species.

Spread of the Zoonotic Nematode Baylisascaris procyonis into a Naive Raccoon Population

The raccoon roundworm (Baylisascaris procyonis), a gastrointestinal nematode of the raccoon (Procyon lotor), may cause a severe form of larva migrans in humans, which can lead to death or permanent neurological damage. Although roundworms were inadvertently introduced to Europe alongside their raccoon hosts, the parasite is not present in every raccoon population. It is important to understand the geographic distribution of B. procyonis, as early and rapid treatment can prevent severe pathologies in humans. We present evidence for the roundworm spreading into a naive raccoon population through natural dispersal of infected raccoons. We sampled 181 raccoons from Saxony-Anhalt, a German federal state containing contact zones of different raccoon populations, two of which were previously free of the parasite. We screened the raccoons for roundworms and used microsatellite-based assignment tests to determine the genetic origin of the raccoons and their parasites. We detected roundworms in 16 of 45 raccoons sampled in a previously roundworm-free area in the northern part of the state. The largest proportion of the genetic ancestry (≥ 0.5) of the 16 raccoon hosts was assigned to the previously naive raccoon population. Conversely, the genetic ancestry of almost all the roundworms was assigned to the nearest roundworm population in the southern part of the state. Infected raccoons have, therefore, spread to the north of the state, where they interbred with and infected local raccoons. It seems likely that the roundworms will continue to spread. Health authorities should consider continuous surveillance programmes of naive populations and raise public awareness.

Microsatellite profiling of hosts from parasite-extracted DNA illustrated with raccoons (Procyon lotor) and their Baylisascaris procyonis roundworms

BACKGROUND

Important information on movement pathways and introduction routes of invasive parasites can be obtained by comparing the genetic makeup of an invader with its spatial genetic structure in other distribution areas. Sometimes, the population genetic structure of the host might be more informative than that of the parasite itself, and it is important to collect tissue samples of both host and parasite. However, host tissue samples are frequently not available for analysis. We aimed to test whether it is possible to generate reliable microsatellite profiles of host individuals by amplifying DNA extracted from a nematode parasite, using the raccoon (Procyon lotor) and the raccoon roundworm (Baylisascaris procyonis) as a test case.

METHODS

Between 2020 and 2021, we collected tissue as well as a single roundworm each from 12 raccoons from central Germany. Both the raccoon and the roundworm DNA extracts were genotyped using 17 raccoon-specific microsatellite loci. For each roundworm DNA extract, we performed at least eight amplification reactions per microsatellite locus.

RESULTS

We extracted amplifiable raccoon DNA from all 12 roundworms. We obtained at least two amplification products for 186 of the 204 possible genotypes. Altogether 1077 of the 1106 genotypes (97.4%) matched the host-DNA derived reference genotypes and thus did not contain genotyping errors. Nine of the 12 roundworm-derived genetic profiles matched the reference profiles from the raccoon hosts, with one additional genetic profile containing genotyping errors at a single locus. The remaining two genetic profiles were deemed unsuitable for downstream analysis because of genotyping errors and/or a high proportion of missing data.

CONCLUSIONS

We showed that reliable microsatellite-based genetic profiles of host individuals can be obtained by amplifying DNA extracted from a parasitic nematode. Specifically, the approach can be applied to reconstruct invasion pathways of roundworms when samples of the raccoon hosts are lacking. Further research should assess whether this method can be replicated in smaller species of parasitic nematodes and other phyla of parasites more generally.

Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal

The major histocompatibility complex (MHC) has been intensively studied for the relative effects of different evolutionary forces in recent decades. Pathogen-mediated balancing selection is generally thought to explain the high polymorphism observed in MHC genes, but it is still unclear to what extent MHC diversity is shaped by selection relative to neutral drift. In this study, we genotyped MHC class II DRB genes and 15 neutral microsatellite loci across 26 geographic populations of European badgers (Meles meles) covering most of their geographic range. By comparing variation of microsatellite and diversity of MHC at different levels, we demonstrate that both balancing selection and drift have shaped the evolution of MHC genes. When only MHC allelic identity was investigated, the spatial pattern of MHC variation was similar to that of microsatellites. By contrast, when functional aspects of the MHC diversity (e.g., immunological supertypes) were considered, balancing selection appears to decrease genetic structuring across populations. Our comprehensive sampling and analytical approach enable us to conclude that the likely mechanisms of selection are heterozygote advantage and/or rare-allele advantage. This study is a clear demonstration of how both balancing selection and genetic drift simultaneously affect the evolution of MHC genes in a widely distributed wild mammal.

Interactions of cranial helminths in the European polecat (Mustela putorius): Implications for host body condition

Multiple helminth species commonly co-occur within mammals and their interactions may negatively affect the survival and breeding success of their hosts. However, it has been difficult to prove competition or mutualism between co-infesting helminths in field studies of wild mammals. The sinus cavities of European polecats (Mustela putorius) can be parasitised by the trematode Troglotrema acutum and the nematode Skrjabingylus nasicola and both helminths can co-occur within hosts. While both parasites can damage the host's bone structure and cause severe pathologies, their impact on host body condition is unclear. It is also unknown whether both parasites interact and how this might affect cranial damage and host body condition. We examined 515 fresh polecat skulls for the presence of both helminths and measured the hosts' amount of kidney perirenal fat as a measure of body condition. Our results demonstrated that, in addition to a host-intrinsic fixed factor (sex) and random factors accounting for spatial and temporal stochasticity, the helminths influenced each other's presence. Infestation with T. acutum increased the probability of catching S. nasicola with increasing age of the host, while males already infested with S. nasicola were more likely to become infested with T. acutum than females infested with the nematode. While we speculate that both effects resulted from parasite-induced behavioural alterations (increased foot consumption), it is not clear why, in the latter case, this effect would be stronger in males than females. We showed that the abundances of both parasites had significant positive effect on the likely presence of skull damage and a significant negative effect on the predicted presence of kidney fat. Given the evolutionary arms race that both host-parasite systems have undergone, it appears unlikely that either helminth played a significant factor in the population decline of the polecat in Europe.

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We provide evidence for interactions between co-infesting helminths in a wild mammal.

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Troglotrema acutum and Skrjabingylus nasicola can co-occur in the skulls of polecats.

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Infestation with one parasite can increase the probability of infestation with the other one.

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Heavy infestation with either helminth may have a negative effect on host body condition.

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Co-infestation does not change the severity of the parasites' clinical impact.

Genomic basis for an informed conservation management of Pelophylax water frogs in Luxembourg

Genetic identification methods have become increasingly important for species that are difficult to identify in the field. A case in point is Pelophylax water frogs. While their morphological determination is highly complex, they include species protected under EU law and some that are classified as invasive. Additionally, genetic data can provide insights into their complex breeding systems, which may or may not involve the reproductive dependency of one species on another. Here, we generate baseline data for water frog monitoring in Luxembourg. We applied a countrywide sampling approach and used SNPs generated by ddRAD sequencing to identify individuals and infer the breeding systems present in the country. We found Pelophylax lessonae and P. kl. esculentus throughout Luxembourg, mostly living in syntopy. In general, a reproductive dependency of P. kl. esculentus on P. lessonae (L‐E system) was revealed. Besides this general system, we detected triploid P. kl. esculentus in six ponds. This indicates a modified L‐E system with reproductive dependency of the triploids on the diploid P. kl. esculentus. The invasive P. cf. bedriagae was detected in three ponds in southern Luxembourg, with evidence for hybridization with native water frogs. In addition to the ddRAD data, we tested a simple genetic method for future monitoring based on the MND1 marker. It showed in almost all cases, an identical species identification as the ddRAD data and was successfully applied to DNA extracts from mouth swabs. Combining this method with our baseline data will enable informed choices for the protection of native water frog species in Luxembourg.

First Record of the Sinus Worm Skrjabingylus petrowi (Nematoda: Metastrongyloidea) in a Pine Marten Martes martes from Poland

BACKGROUND

Skrjabingylus spp. are nematodes that parasitize in the frontal and nasal sinuses of small mustelids. In Europe, the two species S. nasicola and S. petrowi are known, although records of S. petrowi are extremely rare, except in the former part of the USSR. The aim of the present study was to screen pine martens (Martes martes) from Poland for the first time for the presence of S. petrowi.

METHODS

Three road-killed pine martens were collected in 2018 and 2020 in the province Lower Silesian in southwestern Poland. A complete necropsy was performed on the fresh pine marten heads and especially the frontal sinuses and paranasal sinuses were examined for the presence of Skrjabingylus spp. The species identity of the recovered nematodes was determined by morphological measurements and genetic barcoding.

RESULTS

One of three pine martens examined showed infection with 12 Skrjabingylus spp. in the right frontal sinus. Measurements of the spicule length of the males revealed a range of 480-521 µm which is characteristic of S. petrowi. There was a close match between the COI sequence reported here and of S. petrowi sequences reported from Germany.

CONCLUSION

This is the first report of infection of a pine marten with the sinus worm S. petrowi in Poland.

Next-generation phylogeography resolves post-glacial colonization patterns in a widespread carnivore, the red fox (Vulpes vulpes), in Europe

Carnivores tend to exhibit a lack of (or less pronounced) genetic structure at continental scales in both a geographic and temporal sense and this can confound the identification of post-glacial colonization patterns in this group. In this study we used genome-wide data (using genotyping by sequencing [GBS]) to reconstruct the phylogeographic history of a widespread carnivore, the red fox (Vulpes vulpes), by investigating broad-scale patterns of genomic variation, differentiation and admixture amongst contemporary populations in Europe. Using 15,003 single nucleotide polymorphisms (SNPs) from 524 individuals allowed us to identify the importance of refugial regions for the red fox in terms of endemism (e.g., Iberia). In addition, we tested multiple post-glacial recolonization scenarios of previously glaciated regions during the Last Glacial Maximum using an Approximate Bayesian Computation (ABC) approach that were unresolved from previous studies. This allowed us to identify the role of admixture from multiple source population post-Younger Dryas in the case of Scandinavia and ancient land-bridges in the colonization of the British Isles. A natural colonization of Ireland was deemed more likely than an ancient human-mediated introduction as has previously been proposed and potentially points to a larger mammalian community on the island in the early post-glacial period. Using genome-wide data has allowed us to tease apart broad-scale patterns of structure and diversity in a widespread carnivore in Europe that was not evident from using more limited marker sets and provides a foundation for next-generation phylogeographic studies in other non-model species.

Population genetics, invasion pathways and public health risks of the raccoon and its roundworm Baylisascaris procyonis in northwestern Europe

The geographic range of the zoonotic raccoon roundworm (Baylisascaris procyonis) is expanding together with the range of its host, the raccoon (Procyon lotor). This creates a new public health risk in parts of Europe where this parasite was previously absent. In the Netherlands, a raccoon population is becoming established and incidental findings of B. procyonis have been reported. To assess the risk to public health, the prevalence of B. procyonis was determined in the province of Limburg, where currently the largest Dutch raccoon population is present, as well as in the adjoining region of southern Belgium. Furthermore, genetic methods were employed to assess invasion pathways of both the raccoon and B. procyonis to aid in the development of control measures. Macroscopic analysis of intestinal content and testing of faecal samples were performed to detect B. procyonis adults and eggs. The population genetics of both B. procyonis and its raccoon host were analysed using samples from central and northwestern Europe. B. procyonis was found in 14/23 (61%, 95% CI: 41%-78%) raccoons from Limburg, but was not detected in 50 Belgian raccoons. Genetic analyses showed that the majority of the Dutch raccoons and their roundworms were introduced through ex-captive individuals. As long as free-living raccoon populations originate from captivity, population control methods may be pursued. However, natural dispersal from the border regions will complicate prolonged population control. To reduce the public health risk posed by B. procyonis, public education to increase awareness and adapt behaviour towards raccoons is key.

Geographic Distribution of Raccoon Roundworm, Baylisascaris procyonis, Germany and Luxembourg

Infestation with Baylisascaris procyonis, a gastrointestinal nematode of the raccoon, can cause fatal disease in humans. We found that the parasite is widespread in central Germany and can pose a public health risk. The spread of B. procyonis roundworms into nematode-free raccoon populations needs to be monitored.

Zoonotic Giardia duodenalis sub-assemblage BIV in wild raccoons (Procyon lotor) from Germany and Luxembourg

Giardia duodenalis is a cosmopolitan flagellate that causes giardiasis, one of the most significant gastrointestinal diseases in humans. This parasite can be a serious threat to public health because it can cause waterborne outbreaks as well as sporadic infections in humans. Invasive raccoons (Procyon lotor) may play a role in disseminating Giardia into the environment and transmitting it to humans and domestic animals because they live in high densities and deposit their faces in latrines near areas used by humans. While Giardia infections have been reported from raccoons in North America, it is unknown whether they carry G. duodenalis with zoonotic assemblage A and B, which have the potential to cause illness in humans. We collected faecal samples from 66 legally harvested raccoons in Germany and Luxembourg and examined for Giardia using molecular techniques. Using a quantitative PCR based on primers specific to Giardia genetic assemblages A and B, we detected the presence of zoonotic assemblage B in 27% (95% CI, 17.0-39.6) of all examined faecal samples from raccoons, including animals sampled in buildings. We did not detect genetic assemblage A in any of the samples. Sequences obtained from the glutamate dehydrogenase and beta-giardin gene fragments from a selection of three of the positive samples showed that raccoons carried a zoonotic G. duodenalis genotype belonging to sub-assemblage BIV, which is commonly found in humans and animals worldwide. Our results suggest that free-ranging raccoons have the potential to play an increasingly important role in the epidemiology of Giardia and pose a threat to public health in Europe and other regions where this species is common and lives in close association with humans.

A potential zoonotic threat: First detection of Baylisascaris procyonis in a wild raccoon from Austria

Baylisascaris procyonis is a common gastrointestinal parasite of raccoons (Procyon lotor) in their native range, and both have been introduced to Europe. Humans may ingest ascarid eggs shed via the racoons’ faeces, and this could lead to severe infections affecting the central nervous system. Here, we report the first occurrence of B. procyonis in Austria. The parasite was detected in a two‐year‐old male raccoon that was road‐killed in November 2019 near Hittisau (Vorarlberg). Genetic profiling provided strong evidence that the raccoon (and its parasite) originated from the nearest German raccoon population. The first finding in Austria highlights the need for monitoring the parasite and information of the public and practitioners.

Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species' inherent behavioural variability. There are no functional connectivity analyses using continuous individual-based sampling across an urban-rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban-rural landscape. We assessed functional connectivity by applying an individual-based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector-based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built-up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man-made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers.

Selenium and mercury in the hair of raccoons (Procyon lotor) and European wildcats (Felis s. silvestris) from Germany and Luxembourg

This study examined the concentration of total mercury (THg) and selenium (Se), as well as the molar ratio of Se:THg in hair samples of terrestrial animals. THg and Se concentrations were measured from the hair of raccoons (Procyon lotor) and European wildcats (Felis s. silvestris) from Germany and Luxembourg. Median THg concentrations in hair from raccoons and wildcats were 0.369 and 0.273 mg kg-1 dry weight (dw), respectively. Se concentrations were higher in the hair of raccoons than of wildcats (0.851 and 0.641 mg kg-1 dw, respectively). Total mercury concentration in hair of raccoons from Luxembourg was almost 5× higher that found in hair of raccoons from Germany; however, Se concentration was similar. Thus, molar ratio of Se:THg was ~4× higher in the hair of raccoons from Germany than those from Luxembourg. Significant negative correlation was found between THg concentration and Se:THg molar ratio in both wildcats and raccoons.

Serological survey of feline viral pathogens in free-living European wildcats (Felis s. silvestris) from Luxembourg

European populations of free-living wildcats have been shown to be exposed to cat viruses. Luxembourg has a high degree of habitat fragmentation, and hybridisation rates between domestic cats and wildcats are high. We therefore assessed the seroprevalence of six viruses in 34 serum samples collected between 2001 and 2016 from wildcats in Luxembourg. The values for feline leukemia virus (FeLV; 52.9%) and feline coronavirus (FCoV; 47.1%) were amongst the highest reported for wildcats. We found evidence for the cumulative likelihood of exposure to FCoV affecting its seroprevalence. Routine monitoring of viral agents in this strictly protected species should be considered.

First report on the sero-epidemiology of Toxoplasma gondii infection in German roe deer (Capreolus capreolus)

While the roe deer (Capreolus capeolus) is the most important game species in Germany and its venison is popular, there is limited knowledge about the prevalence of Toxoplasma gondii in this animal population in the country, and in wild ungulates in Germany generally. Between 2013 and 2015, we collected 295 blood samples from roe deer belonging to a central German population. Sera were analysed using a modified agglutination test (MAT, cut-off 1:20), and antibodies were detected in 86 of the 295 samples (29%). Seroprevalence values differed significantly between the different age classes, with antibodies more frequently observed in adults. In contrast, seroprevalence did not differ significantly between the sexes or collection years. Venison is frequently consumed raw or undercooked and may be a potential source of human infection with T. gondii.

Seroprevalence of Toxoplasma gondii in free-living European mouflon (Ovis orientalis musimon) hunted in central Germany

Despite increasing consumption of mouflon (Ovis orientalis musimon) meat in Germany, there is currently no surveillance of Toxoplasma gondii infection in populations of these animals and generally little knowledge about the prevalence of this protozoan in German wild ungulates. Between 2011 and 2015, we collected 138 blood samples from a free-living mouflon population in central German and tested sera for the presence of T. gondii antibodies using a modified agglutination test (MAT, cut-off 1:20). Antibodies were detected in 31 of the 138 samples (22.46%). There was a significant difference in seroprevalence between the different age classes, with antibodies to T. gondii more frequent in adults. In contrast, there was no significant difference in seroprevalence depending on sex and year of sample collection. Game meat is frequently consumed as raw or undercooked meat and may therefore represent a potential source of human infection with T. gondii.

Similar yet different: co-analysis of the genetic diversity and structure of an invasive nematode parasite and its invasive mammalian host

Animal parasitic nematodes can cause serious diseases and their emergence in new areas can be an issue of major concern for biodiversity conservation and human health. Their ability to adapt to new environments and hosts is likely to be affected by their degree of genetic diversity, with gene flow between distinct populations counteracting genetic drift and increasing effective population size. The raccoon roundworm (Baylisascaris procyonis), a gastrointestinal parasite of the raccoon (Procyon lotor), has increased its global geographic range after being translocated with its host. The raccoon has been introduced multiple times to Germany, but not all its populations are infected with the parasite. While fewer introduced individuals may have led to reduced diversity in the parasite, admixture between different founder populations may have counteracted genetic drift and bottlenecks. Here, we analyse the population genetic structure of the roundworm and its raccoon host at the intersection of distinct raccoon populations infected with B. procyonis. We found evidence for two parasite clusters resulting from independent introductions. Both clusters exhibited an extremely low genetic diversity, suggesting small founding populations subjected to inbreeding and genetic drift with no, or very limited, genetic influx from population admixture. Comparison of the population genetic structures of both host and parasite suggested that the parasite spread to an uninfected raccoon founder population. On the other hand, an almost perfect match between cluster boundaries also suggested that the population genetic structure of B. procyonis has remained stable since its introduction, mirroring that of its raccoon host.

Using genetic tools to estimate the prevalence of non-native red deer (Cervus elaphus) in a Western European population

Game species like the red deer have been subjected to anthropogenic impacts for centuries. Translocations are often carried out—sometimes illegally—not only for sporting purposes, but also to increase trophy quality, reduce inbreeding, or mitigate bottlenecks after excessive persecution. Apart from the blurring of large‐scale genetic structure, translocations without adequate quarantine measure risk introducing pathogens into potentially immunologically naïve populations. It is therefore important to understand the frequency of clandestine translocations. Identification of non‐autochthonous animals and their potential origin is often difficult and, in red deer, has been hampered by the lack of large‐scale genotypic datasets for comparison. In the present study, we make use of a recently published European‐wide microsatellite dataset to detect and quantify the presence of non‐autochthonous red deer in a large population sample (n = 1,780) from Central Europe (Belgium). Using factorial correspondence analysis, assignment tests and Bayesian clustering algorithms we arrive at an estimate of 3.7% non‐autochthonous animals (or their descendants). Some of these animals were assigned to a nearby French population and may have immigrated into Belgium naturally, but the large majority must have been introduced by humans. Our analysis pointed to the British Isles and Germany/Poland as the potential origin of many introduced deer, regions known to have been source populations for translocations in Europe and beyond. We found evidence for recreational hunters using carcasses from farmed deer to fulfill mandatory hunting quotas. Our study is the first to quantify the extent of human‐mediated introductions in a European game species at such a large scale with large and representative sample sizes.

Identifying a hunter responsible for killing a hunting dog by individual-specific genetic profiling of wild boar DNA transferred to the canine during the accidental shooting

While genetic profiling can be a powerful tool to solve wildlife crime, comparably few examples of individual identification in wildlife forensics are available in the literature. Here, we report a case of an accidental shooting of a hunting dog during a wild boar drive hunt. The market value of trained hunting dogs can reach several thousand euro. No one admitted to killing the dog. Wild boar hairs were found in the dog's wound, suggesting that the bullet first hit a wild boar and then the dog. Since it was known who harvested each boar, we aimed to use individual-specific genetic profiles to link these hairs to a bagged animal and to identify the culprit. We genotyped 19 harvested boar and the unknown hair sample using 13 STRs. In the case of the hair sample, we performed multiple genotyping to ensure the reliability of the genetic profile. We showed that we genotyped sufficient loci to distinguish between separate individuals with certainty. While the three most informative loci were enough to differentiate the 19 reference individuals, we did find a perfect match at all 13 STRs between the hair DNA and one tissue sample. Since our methods were reliable and reproducible, we passed the relevant information on to forestry officials who will use the information we have provided to attempt to find an amicable solution.

Homogenous Population Genetic Structure of the Non-Native Raccoon Dog (Nyctereutes procyonoides) in Europe as a Result of Rapid Population Expansion

The extent of gene flow during the range expansion of non-native species influences the amount of genetic diversity retained in expanding populations. Here, we analyse the population genetic structure of the raccoon dog (Nyctereutes procyonoides) in north-eastern and central Europe. This invasive species is of management concern because it is highly susceptible to fox rabies and an important secondary host of the virus. We hypothesized that the large number of introduced animals and the species' dispersal capabilities led to high population connectivity and maintenance of genetic diversity throughout the invaded range. We genotyped 332 tissue samples from seven European countries using 16 microsatellite loci. Different algorithms identified three genetic clusters corresponding to Finland, Denmark and a large 'central' population that reached from introduction areas in western Russia to northern Germany. Cluster assignments provided evidence of long-distance dispersal. The results of an Approximate Bayesian Computation analysis supported a scenario of equal effective population sizes among different pre-defined populations in the large central cluster. Our results are in line with strong gene flow and secondary admixture between neighbouring demes leading to reduced genetic structuring, probably a result of its fairly rapid population expansion after introduction. The results presented here are remarkable in the sense that we identified a homogenous genetic cluster inhabiting an area stretching over more than 1500km. They are also relevant for disease management, as in the event of a significant rabies outbreak, there is a great risk of a rapid virus spread among raccoon dog populations.

Genetic Structure and Effective Population Sizes in European Red Deer (Cervus elaphus) at a Continental Scale: Insights from Microsatellite DNA

We analyzed more than 600 red deer (Cervus elaphus) from large parts of its European distribution range at 13 microsatellite loci, presenting the first continent-wide study of this species using nuclear markers. Populations were clearly differentiated (overall F ST = 0.166, Jost's D est = 0.385), and the BAPS clustering algorithm yielded mainly geographically limited and adjacent genetic units. When forced into only 3 genetic clusters our data set produced a very similar geographic pattern as previously found in mtDNA phylogeographic studies: a western group from Iberia to central and parts of Eastern Europe, an eastern group from the Balkans to Eastern Europe, and a third group including the threatened relict populations from Sardinia and Mesola in Italy. This result was also confirmed by a multivariate approach to analyzing our data set, a discriminant analysis of principal components. Calculations of genetic diversity and effective population sizes (linkage disequilibrium approach) yielded the lowest results for Italian (Sardinia, Mesola; N e between 2 and 8) and Scandinavian red deer, in line with known bottlenecks in these populations. Our study is the first to present comparative nuclear genetic data in red deer across Europe and may serve as a baseline for future analyses of genetic diversity and structuring in this widespread ungulate.

Historical Invasion Records Can Be Misleading: Genetic Evidence for Multiple Introductions of Invasive Raccoons (Procyon lotor) in Germany

Biological invasions provide excellent study systems to understand evolutionary, genetic and ecological processes during range expansions. There is strong evidence for positive effects of high propagule pressure and the associated higher genetic diversity on invasion success, but some species have become invasive despite small founder numbers. The raccoon (Procyon lotor) is often considered as a typical example for such a successful invasion resulting from a small number of founders. The species' largest non-native population in Germany is commonly assumed to stem from a small number of founders and two separate founding events in the 1930s and 1940s. In the present study we analyzed 407 raccoons at 20 microsatellite loci sampled from the invasive range in Western Europe to test if these assumptions are correct. Contrary to the expectations, different genetic clustering methods detected evidence for at least four independent introduction events that gave rise to genetically differentiated subpopulations. Further smaller clusters were either artifacts or resulted from founder events at the range margin and recent release of captive individuals. We also found genetic evidence for on-going introductions of individuals. Furthermore a novel randomization process was used to determine the potential range of founder population size that would suffice to capture all the alleles present in a cluster. Our results falsify the assumption that this species has become widespread and abundant despite being genetically depauperate and show that historical records of species introductions may be misleading.

Prevalence and molecular identification of the sinus worm Skrjabingylus petrowi (Nematoda: Metastrongyloidea) from Martes spp. in Germany

The nematodes of the genus Skrjabingylus (family Metastrongylidae) can parasitise the nasal and frontal sinus cavities of different carnivore species. Until recently, Skrjabingylus petrowi Bageanov & Petrov, 1941, has mainly been described in pine martens (Martes martes Linnaeus, 1758) and sables (Martes zibellina Linnaeus, 1758) sampled in the European part of the former Soviet Union. Newer finds in the stone marten (Martes foina Erxleben, 1777) and from different parts of Europe suggest, however, that the species might have a broader host-species range than previously assumed and be geographically more widespread as well. Since most S. petrowi records have resulted from chance discoveries rather than systematic surveys, very little is known about the prevalence of S. petrowi in marten populations. Here, we report results of a 20-year extensive survey of fresh marten skulls, where we tested 1.059 marten carcasses originating from 248 localities in Germany for the presence of S. petrowi. We identified an infestation in only four M. martes individuals and one M. foina, despite using a reliable identification method. Based on the spicule lengths of the male nematodes, the parasites were identified as S. petrowi and genetic barcoding confirmed the identification of the samples. In a phylogenetic analysis, S. petrowi and Skrjabingylus nasicola (Leuckart, 1842), formed a sister clade to all the other members of the family Metastrongylidae. The low prevalence of S. petrowi is possibly due to its parasitising in the two marten species that are either not very common (M. martes) or predominantly live in urban habitat (M. foina).

Dissections of fresh skulls confirm low prevalence of Troglotrema acutum (Trematoda: Troglotrematidae) in German badgers (Meles meles)

We examined 131 European badgers Meles meles (Linnaeus, 1758) from 67 localities in central Germany for the presence of the cranial trematode Troglotrema acutum, as previous studies based on museum skulls might have underestimated the prevalence of the parasite in this host. We detected the flatworm in only three individuals that originated from the Rhoen Mountains (Thurigina and Bavaria). While the cranium of one host individual showed the lesions and the sponge-like widening of certain regions of the skullcap that are typical of a T. acutum infection, the skulls of the two remaining badgers did not show any deformations. The three badgers were infected by eight, 20, and 49 T. acutum individuals, respectively. Eggs of the trematode parasite were detected in the paranasal sinuses of two badgers. While badgers infected with T. acutum may not show any surface bone lesions, the results of the present study do not contradict the conclusion that the badger is only an accidental host of T. acutum.

Revisiting the phylogeography and demography of European badgers (Meles meles) based on broad sampling, multiple markers and simulations

Although the phylogeography of European mammals has been extensively investigated since the 1990s, many studies were limited in terms of sampling distribution, the number of molecular markers used and the analytical techniques employed, frequently leading to incomplete postglacial recolonisation scenarios. The broad-scale genetic structure of the European badger (Meles meles) is of interest as it may result from historic restriction to glacial refugia and/or recent anthropogenic impact. However, previous studies were based mostly on samples from western Europe, making it difficult to draw robust conclusions about the location of refugia, patterns of postglacial expansion and recent demography. In the present study, continent-wide sampling and analyses with multiple markers provided evidence for two glacial refugia (Iberia and southeast Europe) that contributed to the genetic variation observed in badgers in Europe today. Approximate Bayesian computation provided support for a colonisation of Scandinavia from both Iberian and southeastern refugia. In the whole of Europe, we observed a decline in genetic diversity with increasing latitude, suggesting that the reduced diversity in the peripheral populations resulted from a postglacial expansion processes. Although MSVAR v.1.3 also provided evidence for recent genetic bottlenecks in some of these peripheral populations, the simulations performed to estimate the method's power to correctly infer the past demography of our empirical populations suggested that the timing and severity of bottlenecks could not be established with certainty. We urge caution against trying to relate demographic declines inferred using MSVAR with particular historic or climatological events.

Closed-population capture-recapture modeling of samples drawn one at a time

Motivated by field sampling of DNA fragments, we describe a general model for capture-recapture modeling of samples drawn one at a time in continuous-time. Our model is based on Poisson sampling where the sampling time may be unobserved. We show that previously described models correspond to partial likelihoods from our Poisson model and their use may be justified through arguments concerning S- and Bayes-ancillarity of discarded information. We demonstrate a further link to continuous-time capture-recapture models and explain observations that have been made about this class of models in terms of partial ancillarity. We illustrate application of our models using data from the European badger (Meles meles) in which genotyping of DNA fragments was subject to error.

Population structure of the mosquito Aedes aegypti (Stegomyia aegypti) in Pakistan

Eleven microsatellite markers were used to determine the genetic population structure and spread of Aedes aegypti (Stegomyia aegypti) (Diptera: Culicidae) in Pakistan using mosquitoes collected from 13 different cities. There is a single genetic cluster of Ae. aegypti in Pakistan with a pattern of isolation by distance within the population. The low level of isolation by distance suggests the long-range passive dispersal of this mosquito, which may be facilitated by the tyre trade in Pakistan. A decrease in genetic diversity from south to north suggests a recent spread of this mosquito from Karachi. A strong negative correlation between genetic distance and the quality of road connections shows that populations in cities connected by better road networks are less differentiated, which suggests the human-aided passive dispersal of Ae. aegypti in Pakistan. Dispersal on a large spatial scale may facilitate the strategy of introducing transgenic Ae. aegypti or intracellular bacteria such as Wolbachia to control the spread of dengue disease in Pakistan, but it also emphasizes the need for simple measures to control container breeding sites.

Comparative landscape genetic analyses show a Belgian motorway to be a gene flow barrier for red deer (Cervus elaphus), but not wild boars (Sus scrofa)

While motorways are often assumed to influence the movement behaviour of large mammals, there are surprisingly few studies that show an influence of these linear structures on the genetic make-up of wild ungulate populations. Here, we analyse the spatial genetic structure of red deer (Cervus elaphus) and wild boars (Sus scrofa) along a stretch of motorway in the Walloon part of Belgium. Altogether, 876 red deer were genotyped at 13 microsatellite loci, and 325 wild boars at 14 loci. In the case of the red deer, different genetic clustering tools identified two genetic subpopulations whose borders matched the motorway well. Conversely, no genetic structure was identified in the case of the wild boar. Analysis of isolation-by-distance patterns of pairs of individuals on the same side and on different sides of the motorway also suggested that the road was a barrier to red deer, but not to wild boar movement. While telemetry studies seem to confirm that red deer are more affected by motorways than wild boar, the red deer sample size was also much larger than that of the wild boars. We therefore repeated the analysis of genetic structure in the red deer with randomly sub-sampled data sets of decreasing size. The power to detect the genetic structure using clustering methods decreased with decreasing sample size.

Using isolation-by-distance-based approaches to assess the barrier effect of linear landscape elements on badger (Meles meles) dispersal

As the European badger (Meles meles) can be of conservation or management concern, it is important to have a good understanding of the species' dispersal ability. In particular, knowledge of landscape elements that affect dispersal can contribute to devising effective management strategies. However, the standard approach of using Bayesian clustering methods to correlate genetic discontinuities with landscape elements cannot easily be applied to this problem, as badger populations are often characterized by a strong confounding isolation-by-distance (IBD) pattern. We therefore developed a two-step method that compares the location of pairs of related badgers relative to a putative barrier and utilizes the expected spatial genetic structure characterized by IBD as a null model to test for the presence of a barrier. If a linear feature disrupts dispersal, the IBD pattern characterising pairs of individuals located on different sides of a putative barrier should differ significantly from the pattern obtained with pairs of individuals located on the same side. We used our new approach to assess the impact of rivers and roads of different sizes on badger dispersal in western England. We show that a large, wide river represented a barrier to badger dispersal and found evidence that a motorway may also restrict badger movement. Conversely, we did not find any evidence for small rivers and roads interfering with badger movement. One of the advantages of our approach is that potentially it can detect features that disrupt gene flow locally, without necessarily creating distinct identifiable genetic units.

Statistical methods in spatial genetics

The joint analysis of spatial and genetic data is rapidly becoming the norm in population genetics. More and more studies explicitly describe and quantify the spatial organization of genetic variation and try to relate it to underlying ecological processes. As it has become increasingly difficult to keep abreast with the latest methodological developments, we review the statistical toolbox available to analyse population genetic data in a spatially explicit framework. We mostly focus on statistical concepts but also discuss practical aspects of the analytical methods, highlighting not only the potential of various approaches but also methodological pitfalls.

Independent colonization of multiple urban centres by a formerly forest specialist bird species

Urban areas are expanding rapidly, but a few native species have successfully colonized them. The processes underlying such colonization events are poorly understood. Using the blackbird Turdus merula, a former forest specialist that is now one of the most common urban birds in its range, we provide the first assessment of two contrasting urban colonization models. First, that urbanization occurred independently. Second, that following initial urbanization, urban-adapted individuals colonized other urban areas in a leapfrog manner. Previous analyses of spatial patterns in the timing of blackbird urbanization, and experimental introductions of urban and rural blackbirds to uncolonized cities, suggest that the leapfrog model is likely to apply. We found that, across the western Palaearctic, urban blackbird populations contain less genetic diversity than rural ones, urban populations are more strongly differentiated from each other than from rural populations and assignment tests support a rural source population for most urban individuals. In combination, these results provide much stronger support for the independent urbanization model than the leapfrog one. If the former model predominates, colonization of multiple urban centres will be particularly difficult when urbanization requires genetic adaptations, having implications for urban species diversity.