Variation of short tandem repeats within and between species belonging to the Canidae family

Assessing the role of individual foxes in environmental contamination with Echinococcus multilocularis through faecal samples

Key parasite transmission parameters are difficult to obtain from elusive wild animals. For Echinococcus multilocularis, the causative agent of alveolar echinococcosis (AE), the red fox is responsible for most of the environmental contamination in Europe. The identification of individual spreaders of E. multilocularis environmental contamination is crucial to improving our understanding of the ecology of parasite transmission in areas of high endemicity and optimising the effectiveness of prevention and control measures in the field. Genetic faecal sampling appears to be a feasible method to gain information about the faecal deposition of individual animals. We conducted a 4 year faecal sampling study in a village that is highly endemic for E. multilocularis, to assess the feasibility of individual identification and sexing of foxes to describe individual infection patterns. Individual fox identification from faecal samples was performed by obtaining reliable genotypes from 14 microsatellites and one sex locus, coupled with the detection of E. multilocularis DNA, first using captive foxes and then by environmental sampling. From a collection of 386 fox stools collected between 2017 and 2020, tested for the presence of E. multilocularis DNA, 180 were selected and 124 samples were successfully genotyped (68.9%). In total, 45 unique individual foxes were identified and 26 associated with at least one sample which tested positive for E. multilocularis (Em(+)). Estimation of the population size showed the fox population to be between 29 and 34 individuals for a given year and 67 individuals over 4 years. One-third of infected individuals (9/26 Em(+) foxes) deposited 2/3 of the faeces which tested positive for E. multilocularis (36/60 Em(+) stools). Genetic investigation showed a significantly higher average number of multiple stools for females than males, suggesting that the two sexes potentially defecated unequally in the studied area. Three partially overlapping clusters of fox faeces were found, with one cluster concentrating 2/3 of the total E. multilocularis-positive faeces. Based on these findings, we estimated that 12.5 million E. multilocularis eggs were produced during the study period, emphasizing the high contamination level of the environment and the risk of exposure faced by the parasite hosts.

Patterns of Wolf Dispersal Respond to Harvest Density across an Island Complex

Wolves are highly mobile predators and can disperse across a variety of habitats and over long distances. However, less is known about dispersal capabilities across water and among islands. The biogeography of island systems fosters spatially structured local populations, and their degree of connectivity may influence the dynamics and long-term viability of the regional population. We sought to quantify wolf dispersal rate, distance, and dispersal sex bias throughout Prince of Wales Island, a 6670 km2 island in southeast Alaska, and the surrounding islands that constitute the wildlife management unit (9025 km2). We also investigated patterns of dispersal in relation to hunting and trapping intensity and wolf population density. We used DNA data collected during 2012-2021 long-term monitoring efforts and genotyped 811 wolves, 144 of which (18%) were dispersers. Annual dispersal rates were 9-23% and had a weakly positive relationship with wolf density. Wolves dispersed 41.9 km on average (SD = 23.7 km), and males and females did not disperse at different rates. Of the dispersing wolves, 107 died, and the majority (n = 81) died before they were able to settle. The leading manner of death was trapping (97% of mortalities), and wolves tended to disperse from areas with low harvest density to areas where harvest density was relatively higher. Dispersal occurred both to and from small islands and the larger Prince of Wales Island, indicating bidirectional as opposed to asymmetrical movement, and the genetic overlap of wolf groups demonstrates connectivity throughout this naturally patchy system. Island ecosystems have different predator-prey dynamics and recolonization processes than large, intact systems due to their isolation and restricted sizes; thus, a better understanding of the degree of population connectivity including dispersal patterns among islands in the Prince of Wales archipelago could help inform the management and research strategies of these wolves.

Genetic Monitoring of Grey Wolves in Latvia Shows Adverse Reproductive and Social Consequences of Hunting

Nowadays, genetic research methods play an important role in animal population studies. Since 2009, genetic material from Latvian wolf specimens obtained through hunting has been systematically gathered. This study, spanning until 2021, scrutinizes the consequences of regulated wolf hunting on population genetic metrics, kinship dynamics, and social organization. We employed 16 autosomal microsatellites to investigate relationships between full siblings and parent-offspring pairs. Our analysis encompassed expected and observed heterozygosity, inbreeding coefficients, allelic diversity, genetic distance and differentiation, mean pairwise relatedness, and the number of migrants per generation. The Latvian wolf population demonstrated robust genetic diversity with minimal inbreeding, maintaining stable allelic diversity and high heterozygosity over time and it is not fragmented. Our findings reveal the persistence of conventional wolf pack structures and enduring kinship groups. However, the study also underscores the adverse effects of intensified hunting pressure, leading to breeder loss, pack disruption, territorial displacement, and the premature dispersal of juvenile wolves.

Variation in adult and pup wolf diets at natal den sites is influenced by forest composition and configuration

Although wolves are wide-ranging generalist carnivores throughout their life cycle, during the pup-rearing season wolf activity is focused on natal den sites where pup survival depends upon pack members provisioning food. Because prey availability is influenced by habitat quality within the home range, we investigated the relative importance of prey species for adults and pups and further examined the relationship between habitat characteristics, wolf diet, and litter size on Prince of Wales Island (POW) in Southeast Alaska. During 2012-2020, we detected 13 active den sites within the home ranges of nine wolf packs. We estimated minimum pup counts using motion-detecting cameras and individual genotypes from noninvasive samples (hair: n = 322; scat: n = 227) and quantified wolf diet composition using fecal DNA metabarcoding (n = 538). We assessed habitat composition, configuration, and connectivity within denning and annual home ranges estimated using wolf GPS-collar data. Contrary to expectations, wolves had a more constricted diet during denning season (April 15-July 31), and within this season pups had a narrower dietary niche (species richness [S] = 4) focused more on deer (relative frequency of occurrence [O/I] = 0.924) than adults (S = 15; deer O/I = 0.591). Litter size had a positive relationship with the relative frequency of deer in a wolf pack's diet. Wolf consumption of deer was positively associated with the proportion of young-growth forest (≤25 years old) within denning and annual home ranges. High levels of vegetation patch interspersion, and the density of closed logging roads were also important predictors, suggesting these habitat qualities were influential for increasing the availability of deer to wolves. Our results contrast with previous research indicating wolf pup diets included more alternate prey (i.e., beaver) than adults and emphasize the importance of deer to wolf viability on POW, especially during denning season.

Wolf Dispersal Patterns in the Italian Alps and Implications for Wildlife Diseases Spreading

Simple Summary

Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. For many species, little is known about dispersal, despite its importance to conservation. We documented the natural dispersal processes of an expanding wolf (Canis lupus) population in the Italian Alps to understand the dynamics of the recolonization pattern and identify diseases that might be connected with the process through the use of non-invasive genetic sampling over a 20-year period. By documenting 55 dispersal events, with an average minimum straight dispersal distance of 65.8 km (±67.7 km), from 7.7 km to 517.2 km, we discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.

Abstract

Wildlife dispersal directly influences population expansion patterns, and may have indirect effects on the spread of wildlife diseases. Despite its importance to conservation, little is known about dispersal for several species. Dispersal processes in expanding wolf (Canis lupus) populations in Europe is not well documented. Documenting the natural dispersal pattern of the expanding wolf population in the Alps might help understanding the overall population dynamics and identifying diseases that might be connected with the process. We documented 55 natural dispersal events of the expanding Italian wolf alpine population over a 20-year period through the use of non-invasive genetic sampling. We examined a 16-locus microsatellite DNA dataset of 2857 wolf samples mainly collected in the Western Alps. From this, we identified 915 individuals, recaptured 387 (42.3%) of individuals, documenting 55 dispersal events. On average, the minimum straight dispersal distance was 65.8 km (±67.7 km), from 7.7 km to 517.2 km. We discussed the potential implications for maintaining genetic diversity of the population and for wildlife diseases spreading.

Settlement of a stable wolf pack in a highly anthropic area of Pisan hills: Relationship with animal husbandry and hunting in a human-wolf coexistence perspective

Anthropic areas play a pivot role for main wolf conservation challenges. Wolf presence in the higher Pisan hills has been well documented while wolf settlement in the lower Pisan hills is still uncertain. In this study, long-term information on wolf presence in a highly anthropic area of the lower Pisan hills was collected by using non-invasive monitoring techniques. Furthermore, both the relationship of this predator with human activity and the impact of hunting on wolf presence have been investigated. The results obtained indicate the presence of a stable and reproductive wolf pack composed by both Italian wolf and hybrids individuals in the municipalities of Crespina Lorenzana and Casciana Terme Lari. A high impact of wolf on livestock was recorded in this area since no prevention systems were adopted by farmers. Wolf appears not to have a negative impact on wild boar population. Similarly, wild boar drive hunting does not appear to affect the wolf pack presence in the area. Thereby wolf may play a key role as controller of wild population. Prevention strategies improvement becomes instrumental to promote wolf-human coexistence. Further investigation to monitor pack hybridization level and turnover and to assess the impact of packs on wild population and livestock in anthropic areas is desirable.

Automated genotyping of microsatellite loci from feces with high throughput sequences

Ecological and conservation genetic studies often use noninvasive sampling, especially with elusive or endangered species. Because microsatellites are generally short in length, they can be amplified from low quality samples such as feces. Microsatellites are highly polymorphic so few markers are enough for reliable individual identification, kinship determination, or population characterization. However, the genotyping process from feces is expensive and time consuming. Given next-generation sequencing (NGS) and recent software developments, automated microsatellite genotyping from NGS data may now be possible. These software packages infer the genotypes directly from sequence reads, increasing throughput. Here we evaluate the performance of four software packages to genotype microsatellite loci from Iberian wolf (Canis lupus) feces using NGS. We initially combined 46 markers in a single multiplex reaction for the first time, of which 19 were included in the final analyses. Megasat was the software that provided genotypes with fewer errors. Coverage over 100X provided little additional information, but a relatively high number of PCR replicates were necessary to obtain a high quality genotype from highly unoptimized, multiplexed reactions (10 replicates for 18 of the 19 loci analyzed here). This could be reduced through optimization. The use of new bioinformatic tools and next-generation sequencing data to genotype these highly informative markers may increase throughput at a reasonable cost and with a smaller amount of laboratory work. Thus, high throughput sequencing approaches could facilitate the use of microsatellites with fecal DNA to address ecological and conservation questions.

How the west was won: genetic reconstruction of rapid wolf recolonization into Germany's anthropogenic landscapes

Following massive persecution and eradication, strict legal protection facilitated a successful reestablishment of wolf packs in Germany, which has been ongoing since 2000. Here, we describe this recolonization process by mitochondrial DNA control-region sequencing, microsatellite genotyping and sex identification based on 1341 mostly non-invasively collected samples. We reconstructed the genealogy of German wolf packs between 2005 and 2015 to provide information on trends in genetic diversity, dispersal patterns and pack dynamics during the early expansion process. Our results indicate signs of a founder effect at the start of the recolonization. Genetic diversity in German wolves is moderate compared to other European wolf populations. Although dispersal among packs is male-biased in the sense that females are more philopatric, dispersal distances are similar between males and females once only dispersers are accounted for. Breeding with close relatives is regular and none of the six male wolves originating from the Italian/Alpine population reproduced. However, moderate genetic diversity and inbreeding levels of the recolonizing population are preserved by high sociality, dispersal among packs and several immigration events. Our results demonstrate an ongoing, rapid and natural wolf population expansion in an intensively used cultural landscape in Central Europe.

Low Persistence of Genetic Rescue Across Generations in the Arctic Fox (Vulpes lagopus)

Genetic rescue can facilitate the recovery of small and isolated populations suffering from inbreeding depression. Long-term effects are however complex, and examples spanning over multiple generations under natural conditions are scarce. The aim of this study was to test for long-term effects of natural genetic rescue in a small population of Scandinavian Arctic foxes (Vulpes lagopus). By combining a genetically verified pedigree covering almost 20 years with a long-term dataset on individual fitness (n = 837 individuals), we found no evidence for elevated fitness in immigrant F2 and F3 compared to native inbred foxes. Population inbreeding levels showed a fluctuating increasing trend and emergence of inbreeding within immigrant lineages shortly after immigration. Between 0–5 and 6–9 years post immigration, the average number of breeding adults decreased by almost 22% and the average proportion of immigrant ancestry rose from 14% to 27%. Y chromosome analysis revealed that 2 out of 3 native male lineages were lost from the gene pool, but all founders represented at the time of immigration were still contributing to the population at the end of the study period through female descendants. The results highlight the complexity of genetic rescue and suggest that beneficial effects can be brief. Continuous gene flow may be needed for small and threatened populations to recover and persist in a longer time perspective.

Relationships between fox populations and rabies virus spread in northern Canada

Rabies spreads in both Arctic (Vulpes lagopus) and red foxes (Vulpes vulpes) throughout the Canadian Arctic but limited wildlife disease surveillance, due to the extensive landmass of the Canadian north and its small widely scattered human population, undermines our knowledge of disease transmission patterns. This study has explored genetic population structure in both the rabies virus and its fox hosts to better understand factors that impact rabies spread. Phylogenetic analysis of 278 samples of the Arctic lineage of rabies virus recovered over 40 years identified four sub-lineages, A1 to A4. The A1 lineage has been restricted to southern regions of the Canadian province of Ontario. The A2 lineage, which predominates in Siberia, has also spread to northern Alaska while the A4 lineage was recovered from southern Alaska only. The A3 sub-lineage, which was also found in northern Alaska, has been responsible for virtually all cases across northern Canada and Greenland, where it further differentiated into 18 groups which have systematically evolved from a common predecessor since 1975. In areas of Arctic and red fox sympatry, viral groups appear to circulate in both hosts, but both mitochondrial DNA control region sequences and 9-locus microsatellite genotypes revealed contrasting phylogeographic patterns for the two fox species. Among 157 Arctic foxes, 33 mitochondrial control region haplotypes were identified but little genetic structure differentiating localities was detected. Among 162 red foxes, 18 control region haplotypes delineated three groups which discriminated among the Churchill region of Manitoba, northern Quebec and Labrador populations, and the coastal Labrador locality of Cartwright. Microsatellite analyses demonstrated some genetic heterogeneity among sampling localities of Arctic foxes but no obvious pattern, while two or three clusters of red foxes suggested some admixture between the Churchill and Quebec-Labrador regions but uniqueness of the Cartwright group. The limited population structure of Arctic foxes is consistent with the rapid spread of rabies virus subtypes throughout the north, while red fox population substructure suggests that disease spread in this host moves most readily down certain independent corridors such as the northeastern coast of Canada and the central interior. Interestingly the evidence suggests that these red fox populations have limited capacity to maintain the virus over the long term, but they may contribute to viral persistence in areas of red and Arctic fox sympatry.

First wolves in Luxembourg since 1893, originating from the Alpine and Central European populations

Considering the spread of the grey wolf (Canis lupus) in Europe over the past 30 years, Luxembourg took some measures to prepare for the return of this apex predator, including the establishment of a management plan that notably addresses the issue of wolf depredation on livestock. Here we present the results of genetic analyses of putative wolf saliva, hair and scat samples collected from or near prey carcasses between 2015 and 2020. In two cases, the wolf was confirmed via DNA analysis: in July 2017 near Garnich and in April 2020 near Niederanven, both assigned to category C1 (hard evidence). A third case was classified as C2 (confirmed observation) based on prey carcass characteristics, while genetic analysis yielded no result. These are the first confirmed records of wolves in Luxemburg since 1893. Moreover, the two C1-cases originated from the Alpine (Garnich) and Central European (Niederanven) populations. Given similar developments in the neighboring countries and regions, we conclude that the area including the Benelux countries as well as Rhineland-Palatinate, Saarland and Northern France may well become a melting pot for wolves of the two aforementioned populations in the coming years and decades.

Jackal in hide: detection dogs show first success in the quest for golden jackal (Canis aureus) scats

Golden jackal (Canis aureus) monitoring in central Europe generates more interest and becomes increasingly important with the species’ appearance in areas where it was previously unestablished. For genetic monitoring of golden jackals via scat collection, the distinction of jackal scats from those of related species such as the red fox (Vulpes vulpes) is crucial: if done incorrectly, it can falsify diet studies or inflate costs of DNA analyses. In this study, we tested the potential benefits of using domestic dogs to specifically find jackal scats. We used trained scat detection dogs to locate and identify golden jackal scats in an area of dense shrubland, with the species’ presence previously confirmed via bioacoustic monitoring. On a total of 133 km of transects covering at least two golden jackal groups, two human-dog teams found 34 putative golden jackal scats. A total of 26 of these were successfully genetically analysed, of which 19 were attributed to 13 individual golden jackals, an accuracy rate of 73%. Our results show that detection dogs can successfully differentiate golden jackal scats from other species. This tool can be applied to detect golden jackal presence and establish more reliable estimates of group number and size than previously determined through bioacoustic stimulation. By combining both methods, questions about family structures and kinship, seasonal differences in habitat use and territory sizes can be answered. The regular use of detection dogs can present an efficient method to monitor golden jackals on a long-term basis and to learn more about their behaviour and population dynamics.

Scent marking in wolves Canis lupus inhabiting managed lowland forests in Poland

In wolves Canis lupus, scent marking plays an important role in territory defence. In Europe, studies on patterns of scent marking in wolves have mostly been conducted in mountains or primeval forests, but since these areas are characterised by low human activity, the impact of people on this behaviour has been neglected. We conducted a study that combined genetic methods with an analysis of the spatial distribution of wolf territory markings in lowland managed forests with high human activity. We found that scent markings are deposited by all members of wolf family groups. Wolves most intensively marked crossroads and their vicinity, especially on roads only accessible for four-wheel drive cars. Our study provides further evidence that crossroads of forest roads play a crucial role in wolf scent marking. The results of our study may be useful during inventories of wolf populations based on collecting indirect signs of their presence or non-invasive genetic sampling.

Dynamic range expansion leads to establishment of a new, genetically distinct wolf population in Central Europe

Local extinction and recolonization events can shape genetic structure of subdivided animal populations. The gray wolf (Canis lupus) was extirpated from most of Europe, but recently recolonized big part of its historical range. An exceptionally dynamic expansion of wolf population is observed in the western part of the Great European Plain. Nonetheless, genetic consequences of this process have not yet been fully understood. We aimed to assess genetic diversity of this recently established wolf population in Western Poland (WPL), determine its origin and provide novel data regarding the population genetic structure of the grey wolf in Central Europe. We utilized both spatially explicit and non-explicit Bayesian clustering approaches, as well as a model-independent, multivariate method DAPC, to infer genetic structure in large dataset (881 identified individuals) of wolf microsatellite genotypes. To put the patterns observed in studied population into a broader biogeographic context we also analyzed a mtDNA control region fragment widely used in previous studies. In comparison to a source population, we found slightly reduced allelic richness and heterozygosity in the newly recolonized areas west of the Vistula river. We discovered relatively strong west-east structuring in lowland wolves, probably reflecting founder-flush and allele surfing during range expansion, resulting in clear distinction of WPL, eastern lowland and Carpathian genetic groups. Interestingly, wolves from recently recolonized mountainous areas (Sudetes Mts, SW Poland) clustered together with lowland, but not Carpathian wolf populations. We also identified an area in Central Poland that seems to be a melting pot of western, lowland eastern and Carpathian wolves. We conclude that the process of dynamic recolonization of Central European lowlands lead to the formation of a new, genetically distinct wolf population. Together with the settlement and establishment of packs in mountains by lowland wolves and vice versa, it suggests that demographic dynamics and possibly anthropogenic barriers rather than ecological factors (e.g. natal habitat-biased dispersal patterns) shape the current wolf genetic structure in Central Europe.

Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

Background

The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive, monophyletic, forest dwelling, social canid distributed across south and Southeast Asia. Severe pressures from habitat loss, prey depletion, disease, human persecution and interspecific competition resulted in global population decline in dholes. Despite a declining population trend, detailed information on population size, ecology, demography and genetics is lacking. Generating reliable information at landscape level for dholes is challenging due to their secretive behaviour and monomorphic physical features. Recent advances in non-invasive DNA-based tools can be used to monitor populations and individuals across large landscapes. In this paper, we describe standardization and validation of faecal DNA-based methods for individual identification of dholes. We tested this method on 249 field-collected dhole faeces from five protected areas of the central Indian landscape in the state of Maharashtra, India.

Results

We tested a total of 18 cross-species markers and developed a panel of 12 markers for unambiguous individual identification of dholes. This marker panel identified 101 unique individuals from faecal samples collected across our pilot field study area. These loci showed varied level of amplification success (57–88%), polymorphism (3–9 alleles), heterozygosity (0.23–0.63) and produced a cumulative misidentification rate or PID_(unbiased) and PID_(sibs) value of 4.7 × 10⁻¹⁰ and 1.5 × 10⁻⁴, respectively, indicating a high statistical power in individual discrimination from poor quality samples.

Conclusion

Our results demonstrated that the selected panel of 12 microsatellite loci can conclusively identify dholes from poor quality, non-invasive biological samples and help in exploring various population parameters. This genetic approach would be useful in dhole population estimation across its range and will help in assessing population trends and other genetic parameters for this elusive, social carnivore.

Consideration of sample source for establishing reliable genetic microsatellite data from mammalian carnivore specimens held in natural history collections

Specimens from natural history collections (NHCs) are increasingly being used for genetic studies and can provide information on extinct populations, facilitate comparisons of historical and contemporary populations, produce baseline data before environmental changes, and elucidate patterns of change. Destructive sampling for DNA may be in disagreement with NHC goals of long-term care and maintenance. Differentiating quality among sample sources can direct destructive sampling to the source predicted to yield the highest quality DNA and most reliable data, potentially reducing damage to specimens, laboratory costs, and genotyping errors. We used the kit fox (Vulpes macrotis) as a model species and evaluated the quality and reliability of genetic data obtained from carnivoran specimens via three different sample sources: cranial bones, nasal bones, and toepads. We quantified variation in microsatellite amplification success and genotyping error rates and assessed the reliability of source-specific genic data. Toepads had the highest amplification success rates and lowest genotyping error rates. Shorter loci had higher amplification success and lower allelic dropout rates than longer loci. There were substantial differences in the reliability of resulting multilocus genotypes. Toepads produced the most reliable data, required the fewest replicates, and therefore, had the lowest costs to achieve reliable data. Our results demonstrate that the quality of DNA obtained from specimens varies by sample source and can inform NHCs when evaluating requests for destructive sampling. Our results suggest that prior to large-scale specimen sampling, researchers should conduct pilot studies to differentiate among source-specific data reliability, identify high performing loci, reduce costs of analyses, and minimize destructive sampling.

Genetic rescue in an inbred Arctic fox (Vulpes lagopus) population

Isolation of small populations can reduce fitness through inbreeding depression and impede population growth. Outcrossing with only a few unrelated individuals can increase demographic and genetic viability substantially, but few studies have documented such genetic rescue in natural mammal populations. We investigate the effects of immigration in a subpopulation of the endangered Scandinavian arctic fox (Vulpes lagopus), founded by six individuals and isolated for 9 years at an extremely small population size. Based on a long-term pedigree (105 litters, 543 individuals) combined with individual fitness traits, we found evidence for genetic rescue. Natural immigration and gene flow of three outbred males in 2010 resulted in a reduction in population average inbreeding coefficient (f), from 0.14 to 0.08 within 5 years. Genetic rescue was further supported by 1.9 times higher juvenile survival and 1.3 times higher breeding success in immigrant first-generation offspring compared with inbred offspring. Five years after immigration, the population had more than doubled in size and allelic richness increased by 41%. This is one of few studies that has documented genetic rescue in a natural mammal population suffering from inbreeding depression and contributes to a growing body of data demonstrating the vital connection between genetics and individual fitness.

Genetic and spatial characterization of the red fox (Vulpes vulpes) population in the area stretching between the Eastern and Dinaric Alps and its relationship with rabies and canine distemper dynamics

Information on the population dynamics of a reservoir species have been increasingly adopted to understand and eventually predict the dispersal patterns of infectious diseases throughout an area. Although potentially relevant, to date there are no studies which have investigated the genetic structure of the red fox population in relation to infectious disease dynamics. Therefore, we genetically and spatially characterised the red fox population in the area stretching between the Eastern and Dinaric Alps, which has been affected by both distemper and rabies at different time intervals. Red foxes collected from north-eastern Italy, Austria, Slovenia and Croatia between 2006–2012, were studied using a set of 21 microsatellite markers. We confirmed a weak genetic differentiation within the fox population using Bayesian clustering analyses, and we were able to differentiate the fox population into geographically segregated groups. Our finding might be due to the presence of geographical barriers that have likely influenced the distribution of the fox population, limiting in turn gene flow and spread of infectious diseases. Focusing on the Italian red fox population, we observed interesting variations in the prevalence of both diseases among distinct fox clusters, with the previously identified Italy 1 and Italy 2 rabies as well as distemper viruses preferentially affecting different sub-groups identified in the study. Knowledge of the regional-scale population structure can improve understanding of the epidemiology and spread of diseases. Our study paves the way for an integrated approach for disease control coupling pathogen, host and environmental data to inform targeted control programs in the future.

Two decades of non-invasive genetic monitoring of the grey wolves recolonizing the Alps support very limited dog introgression

Potential hybridization between wolves and dogs has fueled the sensitive conservation and political debate underlying the recovery of the grey wolf throughout Europe. Here we provide the first genetic analysis of wolf-dog admixture in an area entirely recolonized, the northwestern Alps. As part of a long-term monitoring program, we performed genetic screening of thousands of non-invasive samples collected in Switzerland and adjacent territories since the return of the wolf in the mid-1990s. We identified a total of 115 individuals, only 2 of them showing significant signs of admixture stemming from past interbreeding with dogs, followed by backcrossing. This low rate of introgression (<2% accounting for all wolves ever detected over 1998–2017) parallels those from other European populations, especially in Western Europe (<7%). Despite potential hybridization with stray dogs, few founders and strong anthropogenic pressures, the genetic integrity of the Alpine population has remained intact throughout the entire recolonization process. In a context of widespread misinformation, this finding should reduce conflicts among the different actors involved and facilitate wolf conservation. Real-time genetic monitoring will be necessary to identify potential hybrids and support an effective management of this emblematic population.

Evaluating effective population size and genetic diversity of a declining kit fox population using contemporary and historical specimens

Loss of genetic diversity has serious conservation consequences (e.g., loss of adaptive potential, reduced population viability), but is difficult to evaluate without developing long-term, multigenerational datasets. Alternatively, historical samples can provide insights into changes in genetic diversity and effective population size (N e). Kit foxes (Vulpes macrotis) are a species of conservation concern across much of their range. In western Utah, kit fox abundance has declined precipitously from historical levels, causing concern about population persistence. We analyzed genetic samples from museum specimens and contemporary scats to evaluate temporal changes in (a) genetic diversity and (b) N e for kit foxes in western Utah, and (c) discuss our findings with respect to population risk and conservation. The N e of kit foxes in western Utah has decreased substantially. When compared to established conservation thresholds for N e (e.g., the 50/500 rule), observed levels suggest the population may be at risk of inbreeding depression and local extinction. In contrast, we found no significant decrease in genetic diversity associated with declining N e. We detected evidence of low levels of immigration into the population and suspect genetic diversity may have been maintained by this previously undescribed gene flow from adjacent populations. Low or intermittent immigration may serve to temper the potential short-term negative consequences of low N e. We recommend that kit fox conservation efforts focus on evaluating and maintaining landscape connectivity. We demonstrate how historical specimens can provide a baseline of comparison for contemporary populations, highlighting the importance of natural history collections to conservation during a period of declining funding and support.

Estimating densities for sympatric kit foxes (Vulpes macrotis) and coyotes (Canis latrans) using noninvasive genetic sampling

Kit fox (Vulpes macrotis Merriam, 1888) populations in the Great Basin Desert have declined and are of increasing concern for managers. Increasing coyote (Canis latrans Say, 1823) abundance and subsequent intraguild interactions may be one cause for this decline. Concurrent monitoring of carnivores is challenging and therefore rarely conducted. One possible solution for monitoring elusive carnivores is using noninvasive genetic sampling. We used noninvasive genetic sampling to collect fecal DNA from kit foxes and coyotes and estimate their densities from 2013–2014 in Utah, USA. We identified individuals based on microsatellite genotypes and estimated density with multisession spatially explicit capture–recapture models. Mean kit fox density was 0.02 foxes·km−2, while coyote densities were up to four times greater (0.07–0.08 coyotes·km−2). Kit fox densities were significantly lower than densities in the 1950s but were comparable with estimates from the late 1990s, suggesting that populations may be stabilizing after a precipitous decline. Our kit fox density estimates were among the lowest documented for the species. Our coyote density estimate was the first reported in our region and revealed that despite seemingly high abundance, densities are low compared with other regions. Our results suggested that kit foxes may be able to coexist with coyotes.

Spatial genetic structure in American black bears (Ursus americanus): female philopatry is variable and related to population history

Previously, American black bears (Ursus americanus) were thought to follow the pattern of female philopatry and male-biased dispersal. However, recent studies have identified deviations from this pattern. Such flexibility in dispersal patterns can allow individuals greater ability to acclimate to changing environments. We explored dispersal and spatial genetic relatedness patterns across ten black bear populations-including long established (historic), with known reproduction >50 years ago, and newly established (recent) populations, with reproduction recorded <50 years ago-in the Interior Highlands and Southern Appalachian Mountains, United States. We used spatially explicit, individual-based genetic simulations to model gene flow under scenarios with varying levels of population density, genetic diversity, and female philopatry. Using measures of genetic distance and spatial autocorrelation, we compared metrics between sexes, between population types (historic and recent), and among simulated scenarios which varied in density, genetic diversity, and sex-biased philopatry. In empirical populations, females in recent populations exhibited stronger patterns of isolation-by-distance (IBD) than females and males in historic populations. In simulated populations, low-density populations had a stronger indication of IBD than medium- to high-density populations; however, this effect varied in empirical populations. Condition-dependent dispersal strategies may permit species to cope with novel conditions and rapidly expand populations. Pattern-process modeling can provide qualitative and quantitative means to explore variable dispersal patterns, and could be employed in other species, particularly to anticipate range shifts in response to changing climate and habitat conditions.

Non-invasive genetic monitoring involving citizen science enables reconstruction of current pack dynamics in a re-establishing wolf population

Background

Carnivores are re-establishing in many human-populated areas, where their presence is often contentious. Reaching consensus on management decisions is often hampered by a dispute over the size of the local carnivore population. Understanding the reproductive dynamics and individual movements of the carnivores can provide support for management decisions, but individual-level information can be difficult to obtain from elusive, wide-ranging species. Non-invasive genetic sampling can yield such information, but makes subsequent reconstruction of population history challenging due to incomplete population coverage and error-prone data. Here, we combine a collaborative, volunteer-based sampling scheme with Bayesian pedigree reconstruction to describe the pack dynamics of an establishing grey wolf (Canis lupus) population in south-west Finland, where wolf breeding was recorded in 2006 for the first time in over a century.

Results

Using DNA extracted mainly from faeces collected since 2008, we identified 81 individual wolves and assigned credible full parentages to 70 of these and partial parentages to a further 9, revealing 7 breeding pairs. Individuals used a range of strategies to obtain breeding opportunities, including dispersal to established or new packs, long-distance migration and inheriting breeding roles. Gene flow occurred between all packs but inbreeding events were rare.

Conclusions

These findings demonstrate that characterizing ongoing pack dynamics can provide detailed, locally-relevant insight into the ecology of contentious species such as the wolf. Involving various stakeholders in data collection makes these results more likely to be accepted as unbiased and hence reliable grounds for management decisions.

Electronic supplementary material

The online version of this article (10.1186/s12898-017-0154-8) contains supplementary material, which is available to authorized users.

Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure

Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High‐throughput sequencing (HTS) technologies, such as genotype‐by‐sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization‐based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300‐kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on‐target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer‐read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune‐related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.

Fine-scale population genetic structure of arctic foxes (Vulpes lagopus) in the High Arctic

Objective

The arctic fox (Vulpes lagopus) is a circumpolar species inhabiting all accessible Arctic tundra habitats. The species forms a panmictic population over areas connected by sea ice, but recently, kin clustering and population differentiation were detected even in regions where sea ice was present. The purpose of this study was to examine the genetic structure of a population in the High Arctic using a robust panel of highly polymorphic microsatellites.

Results

We analyzed the genotypes of 210 individuals from Bylot Island, Nunavut, Canada, using 15 microsatellite loci. No pattern of isolation-by-distance was detected, but a spatial principal component analysis (sPCA) revealed the presence of genetic subdivisions. Overall, the sPCA revealed two spatially distinct genetic clusters corresponding to the northern and southern parts of the study area, plus another subdivision within each of these two clusters. The north–south genetic differentiation partly matched the distribution of a snow goose colony, which could reflect a preference for settling into familiar ecological environments. Secondary clusters may result from higher-order social structures (neighbourhoods) that use landscape features to delimit their borders. The cryptic genetic subdivisions found in our population may highlight ecological processes deserving further investigations in arctic foxes at larger, regional spatial scales.

Electronic supplementary material

The online version of this article (10.1186/s13104-017-3002-1) contains supplementary material, which is available to authorized users.

Population expansion and individual age affect endoparasite richness and diversity in a recolonising large carnivore population

The recent recolonisation of the Central European lowland (CEL) by the grey wolf (Canis lupus) provides an excellent opportunity to study the effect of founder events on endoparasite diversity. Which role do prey and predator populations play in the re-establishment of endoparasite life cycles? Which intrinsic and extrinsic factors control individual endoparasite diversity in an expanding host population? In 53 individually known CEL wolves sampled in Germany, we revealed a community of four cestode, eight nematode, one trematode and 12 potential Sarcocystis species through molecular genetic techniques. Infections with zoonotic Echinococcus multilocularis, Trichinella britovi and T. spiralis occurred as single cases. Per capita endoparasite species richness and diversity significantly increased with population size and changed with age, whereas sex, microsatellite heterozygosity, and geographic origin had no effect. Tapeworm abundance (Taenia spp.) was significantly higher in immigrants than natives. Metacestode prevalence was slightly higher in ungulates from wolf territories than from control areas elsewhere. Even though alternative canid definitive hosts might also play a role within the investigated parasite life cycles, our findings indicate that (1) immigrated wolves increase parasite diversity in German packs, and (2) prevalence of wolf-associated parasites had declined during wolf absence and has now risen during recolonisation.

Development and validation of real-time PCR assays based on novel molecular markers for the simultaneous detection and identification of Globodera pallida, G. rostochiensis and Heterodera schachtii

Considering the growing trade of seed potato, reliable diagnostic protocols are required for the detection of regulated nematode species. In this study, a specific and sensitive multiplex Taqman-based real-time PCR method was developed in order to detect and identifyGlobodera pallida,G. rostochiensisandHeterodera schachtii. The newly designed primers and probes enabled the detection of all the target populations tested and with no cross-reaction for closely related non-target species (55 populations tested). The limit of detection (LOD) was one juvenile forG. rostochiensisandG. pallidaand five juveniles forH. schachtii. For monitoring potato cyst nematodes, this analytical tool would extend the number of cyst investigated as five juveniles can be detected among 50 cysts in a sample. Furthermore, this multiplex assay detects DNA of the three targeted species in template DNA obtained directly from float material after nematode extraction from soil.

Wolves Recolonizing Islands: Genetic Consequences and Implications for Conservation and Management

After a long and deliberate persecution, the grey wolf (Canis lupus) is slowly recolonizing its former areas in Europe, and the genetic consequences of this process are of particular interest. Wolves, though present in mainland Estonia for a long time, have only recently started to recolonize the country’s two largest islands, Saaremaa and Hiiumaa. The main objective of this study was to analyse wolf population structure and processes in Estonia, with particular attention to the recolonization of islands. Fifteen microsatellite loci were genotyped for 185 individuals across Estonia. As a methodological novelty, all putative wolf-dog hybrids were identified and removed (n = 17) from the dataset beforehand to avoid interference of dog alleles in wolf population analysis. After the preliminary filtering, our final dataset comprised of 168 “pure” wolves. We recommend using hybrid-removal step as a standard precautionary procedure not only for wolf population studies, but also for other taxa prone to hybridization. STRUCTURE indicated four genetic groups in Estonia. Spatially explicit DResD analysis identified two areas, one of them on Saaremaa island and the other in southwestern Estonia, where neighbouring individuals were genetically more similar than expected from an isolation-by-distance null model. Three blending areas and two contrasting transition zones were identified in central Estonia, where the sampled individuals exhibited strong local differentiation over relatively short distance. Wolves on the largest Estonian islands are part of human-wildlife conflict due to livestock depredation. Negative public attitude, especially on Saaremaa where sheep herding is widespread, poses a significant threat for island wolves. To maintain the long-term viability of the wolf population on Estonian islands, not only wolf hunting quota should be targeted with extreme care, but effective measures should be applied to avoid inbreeding and minimize conflicts with local communities and stakeholders.

Population structure of two rabies hosts relative to the known distribution of rabies virus variants in Alaska

For pathogens that infect multiple species, the distinction between reservoir hosts and spillover hosts is often difficult. In Alaska, three variants of the arctic rabies virus exist with distinct spatial distributions. We tested the hypothesis that rabies virus variant distribution corresponds to the population structure of the primary rabies hosts in Alaska, arctic foxes (Vulpes lagopus) and red foxes (Vulpes vulpes) to possibly distinguish reservoir and spillover hosts. We used mitochondrial DNA (mtDNA) sequence and nine microsatellites to assess population structure in those two species. mtDNA structure did not correspond to rabies virus variant structure in either species. Microsatellite analyses gave varying results. Bayesian clustering found two groups of arctic foxes in the coastal tundra region, but for red foxes it identified tundra and boreal types. Spatial Bayesian clustering and spatial principal components analysis identified 3 and 4 groups of arctic foxes, respectively, closely matching the distribution of rabies virus variants in the state. Red foxes, conversely, showed eight clusters comprising two regions (boreal and tundra) with much admixture. These results run contrary to previous beliefs that arctic fox show no fine-scale spatial population structure. While we cannot rule out that the red fox is part of the maintenance host community for rabies in Alaska, the distribution of virus variants appears to be driven primarily by the arctic fox. Therefore, we show that host population genetics can be utilized to distinguish between maintenance and spillover hosts when used in conjunction with other approaches.

Death by sex in an Australian icon: a continent-wide survey reveals extensive hybridization between dingoes and domestic dogs

Hybridization between domesticated animals and their wild counterparts can disrupt adaptive gene combinations, reduce genetic diversity, extinguish wild populations and change ecosystem function. The dingo is a free-ranging dog that is an iconic apex predator and distributed throughout most of mainland Australia. Dingoes readily hybridize with domestic dogs, and in many Australian jurisdictions, distinct management strategies are dictated by hybrid status. Yet, the magnitude and spatial extent of domestic dog-dingo hybridization is poorly characterized. To address this, we performed a continent-wide analysis of hybridization throughout Australia based on 24 locus microsatellite DNA genotypes from 3637 free-ranging dogs. Although 46% of all free-ranging dogs were classified as pure dingoes, all regions exhibited some hybridization, and the magnitude varied substantially. The southeast of Australia was highly admixed, with 99% of animals being hybrids or feral domestic dogs, whereas only 13% of the animals from remote central Australia were hybrids. Almost all free-ranging dogs had some dingo ancestry, indicating that domestic dogs could have poor survivorship in nonurban Australian environments. Overall, wild pure dingoes remain the dominant predator over most of Australia, but the speed and extent to which hybridization has occurred in the approximately 220 years since the first introduction of domestic dogs indicate that the process may soon threaten the persistence of pure dingoes.

A European Concern? Genetic Structure and Expansion of Golden Jackals (Canis aureus) in Europe and the Caucasus

In the first continent-wide study of the golden jackal (Canis aureus), we characterised its population genetic structure and attempted to identify the origin of European populations. This provided a unique insight into genetic characteristics of a native carnivore population with rapid large-scale expansion. We analysed 15 microsatellite markers and a 406 base-pair fragment of the mitochondrial control region. Bayesian-based and principal components methods were applied to evaluate whether the geographical grouping of samples corresponded with genetic groups. Our analysis revealed low levels of genetic diversity, reflecting the unique history of the golden jackal among Europe’s native carnivores. The results suggest ongoing gene flow between south-eastern Europe and the Caucasus, with both contributing to the Baltic population, which appeared only recently. The population from the Peloponnese Peninsula in southern Greece forms a common genetic cluster with samples from south-eastern Europe (ΔK approach in STRUCTURE, Principal Components Analysis [PCA]), although the results based on BAPS and the estimated likelihood in STRUCTURE indicate that Peloponnesian jackals may represent a distinct population. Moreover, analyses of population structure also suggest either genetic distinctiveness of the island population from Samos near the coast of Asia Minor (BAPS, most STRUCTURE, PCA), or possibly its connection with the Caucasus population (one analysis in STRUCTURE). We speculate from our results that ancient Mediterranean jackal populations have persisted to the present day, and have merged with jackals colonising from Asia. These data also suggest that new populations of the golden jackal may be founded by long-distance dispersal, and thus should not be treated as an invasive alien species, i.e. an organism that is “non-native to an ecosystem, and which may cause economic or environmental harm or adversely affect human health”. These insights into the genetic structure and ancestry of Baltic jackals have important implications for management and conservation of jackals in Europe. The golden jackal is listed as an Annex V species in the EU Habitats Directive and as such, considering also the results presented here, should be legally protected in all EU member states.

Whole Genome Association Study to Detect Single Nucleotide Polymorphisms for Behavior in Sapsaree Dog (Canis familiaris)

The purpose of this study was to characterize genetic architecture of behavior patterns in Sapsaree dogs. The breed population (n = 8,256) has been constructed since 1990 over 12 generations and managed at the Sapsaree Breeding Research Institute, Gyeongsan, Korea. Seven behavioral traits were investigated for 882 individuals. The traits were classified as a quantitative or a categorical group, and heritabilities (h(2)) and variance components were estimated under the Animal model using ASREML 2.0 software program. In general, the h(2) estimates of the traits ranged between 0.00 and 0.16. Strong genetic (r G ) and phenotypic (r P ) correlations were observed between nerve stability, affability and adaptability, i.e. 0.9 to 0.94 and 0.46 to 0.68, respectively. To detect significant single nucleotide polymorphism (SNP) for the behavioral traits, a total of 134 and 60 samples were genotyped using the Illumina 22K CanineSNP20 and 170K CanineHD bead chips, respectively. Two datasets comprising 60 (Sap60) and 183 (Sap183) samples were analyzed, respectively, of which the latter was based on the SNPs that were embedded on both the 22K and 170K chips. To perform genome-wide association analysis, each SNP was considered with the residuals of each phenotype that were adjusted for sex and year of birth as fixed effects. A least squares based single marker regression analysis was followed by a stepwise regression procedure for the significant SNPs (p<0.01), to determine a best set of SNPs for each trait. A total of 41 SNPs were detected with the Sap183 samples for the behavior traits. The significant SNPs need to be verified using other samples, so as to be utilized to improve behavior traits via marker-assisted selection in the Sapsaree population.

Heterozygote deficits in cyst plant-parasitic nematodes: possible causes and consequences

Deviations of genotypic frequencies from Hardy-Weinberg equilibrium (HWE) expectations could reveal important aspects of the biology of populations. Deviations from HWE due to heterozygote deficits have been recorded for three plant-parasitic nematode species. However, it has never been determined whether the observed deficits were due (i) to the presence of null alleles, (ii) to a high level of consanguinity and/or (iii) to a Wahlund effect. The aim of the present work was, while taking into the possible confounding effect of null alleles, to disentangle consanguinity and Wahlund effect in natural populations of those three economically important cyst nematodes using microsatellite markers: Globodera pallida, G. tabacum and Heterodera schachtii, pests of potato, tobacco and sugar beet, respectively. The results show a consistent pattern of heterozygote deficiency in the three nematode species sampled at the spatial scale of the host plant. We demonstrate that the prevalence of null alleles is weak and that heterozygote deficits do not have a single origin. Our results suggested that it is restricted dispersal that leads to heterozygote deficits through both consanguinity and substructure, which effects can be linked to soil movement, cyst density, and the number of generations per year. We discuss potential implications for the durability of plant resistances that are used to protect crops against parasites in which mating between relatives occur. While consanguineous mating leads to homozygosity at all loci, including loci governing avirulence/virulence, which favours the expression of virulence when recessive, the Wahlund effect is expected to have no particular effect on the adaptation of nematodes to resistances.