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Glacial and interglacial periods throughout the Pleistocene have been substantial drivers of change in species distributions. Earlier analyses suggested that modern grey wolves (Canis lupus) trace their origin to a single Late Pleistocene Beringian population that expanded east and westwards, starting c. 25,000 years ago (ya). Here, we examined the demographic and phylogeographic histories of extant populations around the Bering Strait with wolves from two inland regions of the Russian Far East (RFE) and one coastal and two inland regions of North-western North America (NNA), genotyped for 91,327 single nucleotide polymorphisms. Our results indicated that RFE and NNA wolves had a common ancestry until c. 34,400 ya, suggesting that these populations started to diverge before the previously proposed expansion out of Beringia. Coastal and inland NNA populations diverged c. 16,000 ya, concordant with the minimum proposed date for the ecological viability of the migration route along the Pacific Northwest coast. Demographic reconstructions for inland RFE and NNA populations reveal spatial and temporal synchrony, with large historical effective population sizes that declined throughout the Pleistocene, possibly reflecting the influence of broadscale climatic changes across continents. In contrast, coastal NNA wolves displayed a consistently lower effective population size than the inland populations. Differences between the demographic history of inland and coastal wolves may have been driven by multiple ecological factors, including historical gene flow patterns, natural landscape fragmentation, and more recent anthropogenic disturbance.

Wolves (Canis lupus) are generally monitored by visual observations, camera traps, and DNA traces. In this study, we evaluated acoustic monitoring of wolf howls as a method for monitoring wolves, which may permit detection of wolves across longer distances than that permitted by camera traps. We analyzed acoustic data of wolves’ howls collected from both wild and captive ones. The analysis focused on individual and subspecies recognition. Furthermore, we aimed to determine the usefulness of acoustic monitoring in the field given the limited data for Eurasian wolves. We analyzed 170 howls from 16 individual wolves from 3 subspecies: Arctic (Canis lupus arctos), Eurasian (C. l. lupus), and Northwestern wolves (C. l. occidentalis). Variables from the fundamental frequency (f0) (lowest frequency band of a sound signal) were extracted and used in discriminant analysis, classification matrix, and pairwise post-hoc Hotelling test. The results indicated that Arctic and Eurasian wolves had subspecies identifiable calls, while Northwestern wolves did not, though this sample size was small. Identification on an individual level was successful for all subspecies. Individuals were correctly classified with 80%–100% accuracy, using discriminant function analysis. Our findings suggest acoustic monitoring could be a valuable and cost-effective tool that complements camera traps, by improving long-distance detection of wolves.

Augmenting the genetic diversity of small, inbred populations by the introduction of new individuals is often termed “genetic rescue”. An example is the Norwegian Lundehund, a small spitz dog with inbreeding-related health problems that is being crossed with three Nordic breeds, including the Norwegian Buhund. Conservation breeding decisions for the (typically) small number of outcrossed individuals are vital for managing the rescue process, and we genotyped the Lundehund (n = 12), the Buhund (n = 12), their crosses (F1, n = 7) and first-generation backcrosses to the Lundehund (F2, n = 12) with >170,000 single nucleotide polymorphism loci to compare their levels of genetic diversity. We predicted that genome-wide diversity in F2 dogs would be higher than in the Lundehund but lower than in the F1 and the Buhund, and the heterozygosity values showed the expected patterns. We also found that runs of homozygosity, extended chromosomal regions of homozygous genotypes inherited from a common ancestor, were reduced in F2 individuals compared with Lundehund individuals. Our analyses demonstrate the benefits of outcrossing but indicate that some of the acquired genetic diversity is lost following immediate backcrossing. Additional breeding among F2 crosses could therefore merit from further consideration in genetic rescue management.

Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions: We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the thirdgeneration backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales. JH received funding from the Maj and Tor Nessling Foundation, the Finnish Cultural Foundation and Emil Aaltonen Foundation. Laboratory analyses were cofounded by the (LOEWE) program (Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz) of the German Federal State of Hessen. AvT received funding from the Karl und Marie Schack-Stiftung. RG was supported by the Portuguese Foundation for Science and Technology (FCT, DL57/2016). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript.

Parasites are integral to ecosystem functioning yet often overlooked. Improved understanding of host–parasite associations is important, particularly for wide‐ranging species for which host range shifts and climate change could alter host–parasite interactions and their effects on ecosystem function.Among the most widely distributed mammals with diverse diets, gray wolves (Canis lupus) host parasites that are transmitted among canids and via prey species. Wolf–parasite associations may therefore influence the population dynamics and ecological functions of both wolves and their prey. Our goal was to identify large‐scale processes that shape host–parasite interactions across populations, with the wolf as a model organism.By compiling data from various studies, we examined the fecal prevalence of gastrointestinal parasites in six wolf populations from two continents in relation to wolf density, diet diversity, and other ecological conditions.As expected, we found that the fecal prevalence of parasites transmitted directly to wolves via contact with other canids or their excreta was positively associated with wolf density. Contrary to our expectations, the fecal prevalence of parasites transmitted via prey was negatively associated with prey diversity. We also found that parasite communities reflected landscape characteristics and specific prey items available to wolves.Several parasite taxa identified in this study, including hookworms and coccidian protozoans, can cause morbidity and mortality in canids, especially in pups, or in combination with other stressors. The density–prevalence relationship for parasites with simple life cycles may reflect a regulatory role of gastrointestinal parasites on wolf populations. Our result that fecal prevalence of parasites was lower in wolves with more diverse diets could provide insight into the mechanisms by which biodiversity may regulate disease. A diverse suite of predator–prey interactions could regulate the effects of parasitism on prey populations and mitigate the transmission of infectious agents, including zoonoses, spread via trophic interactions., Parasites are central to ecosystems but often overlooked. We investigated broad‐scale interactions between gastrointestinal parasites and their hosts by sampling the widely distributed gray wolf (Canis lupus) across six populations on two continents. As expected, wolf density was positively associated with the prevalence of fecal parasites transmitted directly between hosts. Contrary to our expectations, wolves with more diverse diets had a lower prevalence of fecal parasites transmitted via prey, an association that may reflect one mechanism by which biodiversity could influence infection patterns in hosts.

The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species’ unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.

The gray wolf Canis lupus range in central Europe is dynamically expanding, reconnecting previously isolated populations. Thus, a recent paper has proposed to merge the current Baltic and Central European (CE) wolf management units, which are no longer isolated by distance. However, recent genetic findings indicate that these two populations are not genetically homogenous. Here we review the most recent data on wolf genetic structure in central Europe and show that even though the CE and Baltic wolves represent the same phylogeographic lineage, their demographic history has resulted in significant genetic structure between these two populations. While the groups are interconnected by moderate gene flow, it is not high enough to reduce the strong founder signal observed in the CE population, suggesting that population dynamics within the CE wolf range are largely independent from those of its source (Baltic) population. Consequently, a management unit combining the CE and Baltic wolves would not form a demographically coherent entity. Thus, we recommend that conservation management units maintain their separate status.

The Carpathian Mountains provide critical wildlife habitat in central Europe, and previous genome-wide studies have found western Carpathian Mountain wolves (Canis lupus) to be a separate population. Whereas differentiation to the north may be explained by a lowland-mountain transition and habitat fragmentation, the eastern Carpathian Mountains extending through Romania appear to offer continuous wildlife habitat southward. Our objective was to assess gene flow patterns and population connectivity among wolves in Romania, western Ukraine, and the Republic of Moldova. We sought to determine if the Carpathian Mountain region is best described by a north–south gradient in genetic profiles, or whether Romanian wolves show population structure with northern individuals clustering with western Ukraine. We genotyped 48 individuals with 170 000 single nucleotide polymorphism markers, and successful profiles from Romania (n = 27) and Moldova (n = 2) were merged with existing data from western Ukraine (n = 10). Expected heterozygosity was 0.234 (SE 0.001) for Romania and 0.229 (SE 0.001) for western Ukraine, whereas observed heterozygosity values were 0.230 (SE 0.001) versus 0.231 (SE 0.001). Population structure analyses with a maximum likelihood method supported K = 1 population, followed by K = 2 where Romania formed one cluster, and western Ukraine and Moldova formed another. Principal component analysis results were broadly consistent with K = 2. Pairwise FST between western Ukraine and Romania was 0.042 (p = 0.001). Our findings indicated weak population differentiation, and future research may clarify whether the spatial distribution of genetic diversity in the region is associated with environmental and ecological factors such as terrain ruggedness and the distribution of prey species.

Hybridisation between wild and domestic taxa raises complex questions for conservation. Genetic advances offer new methods for hybrid identification, yet social and cultural factors can influence study design, and the interpretation, application, and communication of results. A relevant illustration is hybridisation between domestic dogs (Canis lupus familiaris) and wild canids, such as grey wolves (C. lupus). For regional European monitoring programs in areas with expanding wolf populations, priorities include shared genetic markers and inclusion of all relevant reference populations to ensure dispersing wolves are identified as such and not classified as wolf-dog hybrids, which may cause harmful management decisions. Beyond technical developments, hybrid research and conservation management can benefit from improved integration of legal and policy perspectives, recognition of phenotypic traits as broadly unreliable for identification, and attention to the drivers of, and responses to, evolution in human-dominated landscapes. Additionally, the proliferation of unsubstantiated reports about hybrids in popular and social media shows that communication based on verified findings of hybridisation is essential. Hybridisation requires more constructive discussion on how to balance potentially competing conservation objectives, and the integration of multidisciplinary perspectives. These encompass the welfare of individual animals and preservation of historical predator-prey relationships. Conservation measures centred on preserving the ecological function of wild canids likely offer the most sustainable prospects but require improved understanding of the extent to which their behavioural ecology might differ from that of hybrids. Accurate genetic identification is required to fill this critical knowledge gap, advance public discourse, and initiate relevant conservation actions.

Necrotic inflammation of the prepuce (NIP, posthitis) is probably the most serious threat to the males of European bison (Bison bonasus) population living in the Białowieża National Park. Approximately 6% of the males have been affected every year. The aim of this study was to explore genetic regions potentially affecting this disease. The population was divided into two groups: healthy (25) and affected by posthitis (112). All individuals were genotyped with the Illumina BovineHD BeadChip. Tests performed on a single-locus mixed model (EMMAX) resulted in one SNP on the 25th chromosome (rs134172402) showing statistically important association with the posthitis incidence. The closest candidate gene located near this SNP was the periplakin (PPL) coding protein associated with skin development and some autoimmunity skin diseases such as pemphigus foliaceus or atopic dermatitis. Therefore, we conclude that PPL might be the candidate gene for posthitis, but further studies are necessary to confirm its expression and role in affected tissues.

In 2009, a frozen mummy of the steppe bison (SB) (Bison priscus) was discovered between the lower Kolyma River and the Alazeya River in northeast Siberia, Russia. The specimen was dated with 14C and estimated to have lived more than 48,000 14C years before present (BP). The relationship between SB and the European Bison (EB) (Bison bonasus), also known as wisent or European wood bison, is unresolved and it is unclear whether the SB and EB overlapped in space and time. The aim of our study was to compare genetic variability between the SB specimen and modern EB. We expected higher SB variability due to substantial bottlenecks in the EB approximately one century ago when it became extinct in the wild. The EB (n = 167) and the SB specimen were genotyped with the Illumina BovineHD BeadChip with 777,962 single-nucleotide polymorphism (SNP) markers. Steppe bison DNA was extracted and genotyped six times to account for genotyping errors due to low-quality DNA. We obtained a final set of 7786 SNPs. The mean number of private alleles in EB was 0.027 (± 0.0002) and in SB, it was 0.288 (± 0.0006). This could be explained by factors including differences between species, spatiotemporal divergence, and bottleneck effects. Investigation of historic EB samples could help resolve phylogenetic relationships, the role of the recent bottleneck, and provide information for conservation management to reduce the incidence of disease in the population and maintain its evolutionary potential.

Species range expansions and (re)colonization of landscapes variously dominated by humans occur on a global scale. Understanding such range enlargements and subsequent changes in the composition of ecological communities is important for conservation management, and the golden jackal (Canis aureus) can be considered a model species for regional and continental range expansion. Although this mesopredator has been known from the Adriatic Coast of southeastern Europe for over 500 years, the species is a recent arrival further north, including in Slovenia where jackals were first confirmed in the 1950s. Research from eastern Italy found jackals with ancestry from the Dalmatian region on the Adriatic Coast and the Pannonian region further east. We predicted similar ancestry for Slovenian jackals, and examined samples from Croatia, including Dalmatia and interior regions, Serbia, Hungary, and Slovenia with 25 microsatellite markers to determine population genetic structure. We detected two distinct genetic clusters, representing the Dalmatian and Balkan-Pannonian (Pannonian) jackal populations (FST = 0.157, 95% CI: 0.112–0.209). Contrary to expectations, only few individuals in Slovenia exhibited signs of Dalmatian ancestry, and none appeared to be direct immigrants. Some results suggested a third cluster centered in northern Hungary. These divergent profiles might indicate immigration from outside the study area, and samples from regions further east are required for additional resolution. Based on our results, we hypothesize that Dalmatia has not been a substantial source for recent range expansion of the species, which has likely occurred from the east. Further investigation can help resolve the ancestry and current distribution of the Dalmatian and Pannonian populations, and the ecological relationships resulting from progressively overlapping distributions of canid species. Finally, genomic research could illuminate whether genetic variants from eastern areas might have facilitated jackal expansion into regions characterized by a colder climate, the presence of snow, and extensive forest cover; habitats seemingly avoided by the jackals occupying the Adriatic Coast and surrounding areas in southeastern Europe.

Native domestic breeds represent important cultural heritage and genetic diversity relevant for production traits, environmental adaptation and food security. However, risks associated with low effective population size, such as inbreeding and genetic drift, have elevated concerns over whether unique within‐breed lineages should be kept separate or managed as one population. As a conservation genomic case study of the genetic diversity represented by native breeds, we examined native and commercial cattle (Bos taurus) breeds including the threatened Danish Jutland cattle. We examined population structure and genetic diversity within breeds and lineages genotyped across 770K single nucleotide polymorphism loci to determine (a) the amount and distribution of genetic diversity in native breeds, and (b) the role of genetic drift versus selection. We further investigated the presence of outlier loci to detect (c) signatures of environmental selection in native versus commercial breeds, and (d) native breed adaptation to various landscapes. Moreover, we included older cryopreserved samples to determine (e) whether cryopreservation allows (re)introduction of original genetic diversity. We investigated a final set of 195 individuals and 677K autosomal loci for genetic diversity within and among breeds, examined population structure with principal component analyses and a maximum‐likelihood approach and searched for outlier loci suggesting artificial or natural selection. Our findings demonstrate the potential of genomics for identifying the uniqueness of native domestic breeds, and for maintaining their genetic diversity and long‐term evolutionary potential through conservation plans balancing inbreeding with carefully designed outcrossing. One promising opportunity is the use of cryopreserved samples, which can provide important genetic diversity for populations with few individuals, while helping to preserve their traditional genetic characteristics. Outlier tests for native versus commercial breeds identified genes associated with climate adaptation, immunity and metabolism, and native breeds may carry genetic variation important for animal health and robustness in a changing climate.

A ‘rewilding’ process is occurring in Europe and beyond, centered on landscapes reverting from agricultural use to a more natural state. Wild species are arriving by natural or human-mediated range expansion, at times reclaiming ranges from which they were lost centuries ago. Recent colonizers include alien invasives and species expanding their historical distribution without direct human assistance. These events can deepen our understanding of contemporary evolution, including wildlife responses to changing climatic conditions. Rewilding can advance conservation genomics by encouraging study of wildlife in environments where these species represent novel arrivals or return after prolonged absences. Such efforts could facilitate more experimental approaches to research design than that typically feasible for landscape-scale ecological and evolutionary studies. Correspondingly, developments in conservation genomics offer unparalleled means for testing predictions about rewilding, and advancing evolutionary enlightened and proactive conservation planning. In this perspective article, we examine four European carnivore species relevant as case studies of (re)colonization and/or rewilding, and discuss examples of emerging research opportunities in genomics, evolutionary ecology, and human-wildlife relationships. Keywords: Conservation planning, Dispersal, Evolutionary ecology, Human-modified landscapes, Local adaptation

Anthropogenic hybridization is widely perceived as a threat to the conservation of biodiversity. Nevertheless, to date, relevant policy and management interventions are unresolved and highly convoluted. While this is due to the inherent complexity of the issue, we hereby hypothesize that a lack of agreement concerning management goals and approaches, within the scientific community, may explain the lack of social awareness on this phenomenon, and the absence of effective pressure on decision-makers. By focusing on wolf x dog hybridization in Europe, we hereby (a) assess the state of the art of issues on wolf x dog hybridization within the scientific community, (b) assess the conceptual bases for different viewpoints, and (c) provide a conceptual framework aiming at reducing the disagreements. We adopted the Delphi technique, involving a three-round iterative survey addressed to a selected sample of experts who published at Web of Science listed journals, in the last 10 years on wolf x dog hybridization and related topics. Consensus was reached that admixed individuals should always be defined according to their genetic profile, and that a reference threshold for admixture (i.e., q-value in assignment tests) should be formally adopted for their identification. To mitigate hybridization, experts agreed on adopting preventive, proactive and, when concerning small and recovering wolf populations, reactive interventions. Overall, experts' consensus waned as the issues addressed became increasingly practical, including the adoption of lethal removal. We suggest three non-mutually exclusive explanations for this trend: (i) value-laden viewpoints increasingly emerge when addressing practical issues, and are particularly diverging between experts with different disciplinary backgrounds (e.g., ecologists, geneticists); (ii) some experts prefer avoiding the risk of potentially giving carte blanche to wolf opponents to (illegally) remove wolves, based on the wolf x dog hybridization issue; (iii) room for subjective interpretation and opinions result from the paucity of data on the effectiveness of different management interventions. These results have management implications and reveal gaps in the knowledge on a wide spectrum of issues related not only to the management of anthropogenic hybridization, but also to the role of ethical values and real-world management concerns in the scientific debate.

The grey wolf (Canis lupus) is an iconic large carnivore that has increasingly been recognized as an apex predator with intrinsic value and a keystone species. However, wolves have also long represented a primary source of human–carnivore conflict, which has led to long-term persecution of wolves, resulting in a significant decrease in their numbers, genetic diversity and gene flow between populations. For more effective protection and management of wolf populations in Europe, robust scientific evidence is crucial. This review serves as an analytical summary of the main findings from wolf population genetic studies in Europe, covering major studies from the ‘pre-genomic era’ and the first insights of the ‘genomics era’. We analyse, summarize and discuss findings derived from analyses of three compartments of the mammalian genome with different inheritance modes: maternal (mitochondrial DNA), paternal (Y chromosome) and biparental [autosomal microsatellites and single nucleotide polymorphisms (SNPs)]. To describe large-scale trends and patterns of genetic variation in European wolf populations, we conducted a meta-analysis based on the results of previous microsatellite studies and also included new data, covering all 19 European countries for which wolf genetic information is available: Norway, Sweden, Finland, Estonia, Latvia, Lithuania, Poland, Czech Republic, Slovakia, Germany, Belarus, Russia, Italy, Croatia, Bulgaria, Bosnia and Herzegovina, Greece, Spain and Portugal. We compared different indices of genetic diversity in wolf populations and found a significant spatial trend in heterozygosity across Europe from south-west (lowest genetic diversity) to north-east (highest). The range of spatial autocorrelation calculated on the basis of three characteristics of genetic diversity was 650−850 km, suggesting that the genetic diversity of a given wolf population can be influenced by populations up to 850 km away. As an important outcome of this synthesis, we discuss the most pressing issues threatening wolf populations in Europe, highlight important gaps in current knowledge, suggest solutions to overcome these limitations, and provide recommendations for science-based wolf conservation and management at regional and Europe-wide scales.

Accurate identification of species and populations is essential for biodiversity conservation and for monitoring of international trade in wild species. Morphological and behavioural traits are not always reliable for species identification of samples of unknown origin, and suspected hybridization augments this challenge. We used mitochondrial DNA (mtDNA) markers to identify 24 canid skins illegally imported from Mongolia to Denmark in 1997. Our results indicated that the skins included both wolf (Canis lupus) and dog (Canis lupus familiaris) haplotypes. One of the wolf haplotypes was new. A phylogenetic analysis revealed that the skins shared haplotypes with wolves in Europe and Mongolia, which appears to support the assumption of a Mongolic origin though a different provenance cannot be excluded. We observed an apparent discrepancy between the skins’ morphological traits and the mtDNA identification for 10 out of 24 individuals. This might suggest the presence of hybrids, but poor quality DNA precluded reliable microsatellite typing to investigate hybridization. At present, the scarcity of published records for wolf mtDNA sequences from central Asia limits more detailed investigation and we recommend increased efforts to document genetic variation in this region.

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.

The golden jackal (Canis aureus) is expanding its range across Europe. This process includes ongoing colonization of Slovenia, which may be occurring from the Dalmatian population on the Adriatic Coast and/or the Pannonian Basin population to the east. We analysed genetic profiles from tissue samples collected in Slovenia (n=20), Dalmatia (n=21), northern (n=21) and eastern (n=7) Croatia, and Serbia (n=30) to determine local genetic diversity and the relative influence of the two potential source populations. We examined 15 microsatellite genetic markers already used in national wolf (C. lupus) genetic monitoring, and screened for possible hybrids with reference profiles from wolves and dogs (C. l. familiaris). Our results support the presence of two population clusters ; Dalmatia (n = 21) and a second cluster comprising animals sampled in and around the Panonnian Basin (n = 78). Jackals sampled in Slovenia were primarily assigned to the Pannonian population, although at least four jackals showed sign of Dalmatian ancestry. None of the profiles showed sign of (dog/wolf x jackal) hybrid ancestry. For the Dalmatian population, the average number of alleles per locus (allelic diversity ; Na) was 3.200 (SE 0.279), the observed heterozygosity (Ho) was 0.470 (SE 0.056) and unbiased expected heterozygosity (uHe) was 0.493 (0.051). For the Pannonian population, Na was 4.400 (0.434), Ho was 0.571 (SE 0.043) and uHe was 0.592 (0.038). Future investigation can help clarify whether the pattern of Pannonian-dominated immigration may be changing over time. Moreover, we recommend further study of the ecological function of jackals, their interactions with humans and domestic livestock, and continued monitoring to allow detection of possible hybridization with other canid species. Finally, we found jackal DNA at 21 damage cases during 2013-2018, and there are altogether 30 noninvasive genetic samples where we can confirm jackal presence based on diagnostic alleles. Among these, 20 samples have genotype quality that will allow inclusion in future genetic analyses.

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.

Genetic rescue, outcrossing with individuals from a related population, is used to augment genetic diversity in populations threatened by severe inbreeding and extinction. The endangered Norwegian Lundehund dog underwent at least two severe bottlenecks in the 1940s and 1960s that each left only five inbred dogs, and the approximately 1500 dogs remaining world-wide today appear to descend from only two individuals. The Lundehund has a high prevalence of a gastrointestinal disease, to which all remaining dogs may be predisposed. Outcrossing is currently performed with three Nordic Spitz breeds: Norwegian Buhund, Icelandic Sheepdog, and Norrbottenspets. Examination of single nucleotide polymorphism (SNP) genotypes based on 165K loci in 48 dogs from the four breeds revealed substantially lower genetic diversity for the Lundehund (HE 0.035) than for other breeds (HE 0.209–0.284). Analyses of genetic structure with > 15K linkage disequilibrium-pruned SNPs showed four distinct genetic clusters. Pairwise FST values between Lundehund and the candidate breeds were highest for Icelandic Sheepdog, followed by Buhund and Norrbottenspets. We assessed the presence of outlier loci among candidate breeds and examined flanking genome regions (1 megabase) for genes under possible selection to identify potential adaptive differences among breeds; outliers were observed in flanking regions of genes associated with key functions including the immune system, metabolism, cognition and physical development. We suggest crossbreeding with multiple breeds as the best strategy to increase genetic diversity for the Lundehund and to reduce the incidence of health problems. For this project, the three candidate breeds were first selected based on phenotypes and then subjected to genetic investigation. Because phenotypes are often paramount for domestic breed owners, such a strategy could provide a helpful approach for genetic rescue and restoration of other domestic populations at risk, by ensuring the involvement of owners, breeders and managers at the start of the project. © 2017 Stronen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Understanding the mechanisms and patterns involved in population recoveries is challenging and important in shaping conservation strategies. We used a recovering rear-edge population of brown bears at their southernmost European range in Greece as a case study (2007-2010) to explore the recovery genetics at a species' distribution edge. We used 17 microsatellite and a mitochondrial markers to evaluate genetic structure, estimate effective population size and genetic diversity, and infer gene flow between the identified subpopulations. To understand the larger picture, we also compared the observed genetic diversity of each subpopulation with other brown bear populations in the region. The results indicate that the levels of genetic diversity for bears in western Greece are the lowest recorded in southeastern Europe, but still higher than those of other genetically depauperate bear populations. Apart from a complete separation of bear populations in eastern and western Greece, our results also indicate a considerable genetic sub-structuring in the West. As bear populations in Greece are now recovering, this structure is dissolving through a "recovery cascade" of asymmetric gene flow from South to North between neighboring subpopulations, mediated mainly by males. Our study outlines the importance of small, persisting populations, which can act as "stepping stones" that enable a rapid population expansion and recovery. This in turn makes their importance much greater than their numeric or genetic contribution to a species as a whole.

Context: Methods for detecting contemporary, fine-scale population genetic structure in continuous populations are scarce. Yet such methods are vital for ecological and conservation studies, particularly under a changing landscape. Objectives: Here we present a novel, spatially explicit method that we call landscape relatedness (LandRel). With this method, we aim to detect contemporary, fine-scale population structure that is sensitive to spatial and temporal changes in the landscape. Methods: We interpolate spatially determined relatedness values based on SNP genotypes across the landscape. Interpolations are calculated using the Bayesian inference approach integrated nested Laplace approximation. We empirically tested this method on a continuous population of brown bears (Ursus arctos) spanning two counties in Sweden. Results: Two areas were identified as differentiated from the remaining population. Further analysis suggests that inbreeding has occurred in at least one of these areas. Conclusions: LandRel enabled us to identify previously unknown fine-scale structuring in the population. These results will help direct future research efforts, conservation action and aid in the management of the Scandinavian brown bear population. LandRel thus offers an approach for detecting subtle population structure with a focus on contemporary, fine-scale analysis of continuous populations. © The Author(s) 2016. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

SummaryMany domestic breeds face challenges concerning genetic variability, because of their small population sizes along with a high risk of inbreeding. Therefore, it is important to obtain knowledge on their extinction risk, along with the possible benefits of certain breeding strategies. Since many domestic breeds face the same problems, results from such studies can be applied across breeds and species. Here a Population Viability Analysis (PVA) was implemented to simulate the future probability of extinction for a population of the endangered Danish Jutland cattle (Bos taurus), based on the software Vortex. A PVA evaluates the extinction risk of a population by including threats and demographic values. According to the results from the PVA the population will go extinct after 122 years with the current management. Four scenarios were created to investigate which changes in the breeding scheme would have the largest effect on the survival probabilities, including Scenario 1: More females in the breeding pool, scenario 2: More males in the breeding pool, scenario 3: Increased carrying capacity, and scenario 4: Supplementing males to the population through artificial insemination using semen from bulls used in the populations in past generations. All scenarios showed a positive effect on the population's probability of survival, and with a combination of the different scenarios, the population size seems to be stabilized.

Hybridization processes are widespread throughout the taxonomic range and require conservation recognition. Science can help us understand hybridization processes but not whether and when we ought to conserve hybrids. Important questions include the role of humans in hybridization and the value we place on natural and human-induced hybrids concerning their ecological function. Certain hybrids resulting from human actions have replaced the ecological role of extirpated or extinct parent taxa and this ecological role should be preserved. Conservation policies must increasingly recognize populations of wild organisms that hybridize naturally within the context of their historical ecological role. Natural selection acts on individual organisms and the range of characteristics displayed by individual hybrids constitute raw material for evolution. Guidelines must consider the conservation value of individuals and the ethical aspects of removing hybrids for the purpose of conserving population genetic integrity. Conservation policies should focus on protecting the ecological role of taxa affected by hybridization. An informative example is North American canids (Canis), where body size, prey availability, and human landscape modifications may interact and impose local selective pressures. Gray wolves (Canis lupus) and eastern wolves (Canis lycaon or Canis lupus lycaon) or Great Lakes wolves appear to hybridize naturally within the context of their historical ecological role. In contrast, eastern coyotes (C. latrans) exhibit wolf ancestry and have partly replaced the ecological role of an extirpated parent taxa in parts of northeastern North America. The need for advancing conservation policies that reflect our current understanding of ecology and evolution is urgent.

This investigation presents results from a genetic characterization of 5 Danish dog breeds genotyped on the CanineHD BeadChip microarray with 170,000 SNP. The breeds investigated were 1) Danish Spitz (DS; n=8), 2) Danish-Swedish Farm Dog (DSF; n=18), 3) Broholmer (BR; n=22), 4) Old Danish Pointing Dog (ODP; n=24), and 5) Greenland Dog (GD; n=23). The aims of the investigation were to characterize the genetic profile of the abovementioned dog breeds by quantifying the genetic differentiation among them and the degree of genetic homogeneity within breeds. The genetic profile was determined by means of principal component analysis (PCA) and through a Bayesian clustering method. Both the PCA and the Bayesian clustering method revealed a clear genetic separation of the 5 breeds. The level of genetic variation within the breeds varied. The expected heterozygosity (HE) as well as the degree of polymorphism (P%) ranked the dog breeds in the order DS>DSF>BR>ODP>GD. Interestingly, the breed with a tenfold higher census population size compared to the other breeds, the Greenland Dog, had the lowest within-breed genetic variation, emphasizing that census size is a poor predictor of genetic variation. The observed differences in variation among and within dog breeds may be related to factors such as genetic drift, founder effects, genetic admixture, and population bottlenecks. We further examined whether the observed genetic patterns in the 5 dog breeds can be used to design breeding strategies for the preservation of the genetic pool of these dog breeds.

peer-reviewed Runs of homozygosity (ROH), uninterrupted stretches of homozygous genotypes resulting from parents transmitting identical haplotypes to their offspring, have emerged as informative genome-wide estimates of autozygosity (inbreeding). We used genomic profiles based on 698 K single nucleotide polymorphisms (SNPs) from nine breeds of domestic cattle (Bos taurus) and the European bison (Bison bonasus) to investigate how ROH distributions can be compared within and among species. We focused on two length classes: 0.5–15 Mb to investigate ancient events and >15 Mb to address recent events (approximately three generations). For each length class, we chose a few chromosomes with a high number of ROH, calculated the percentage of times a SNP appeared in a ROH, and plotted the results. We selected areas with distinct patterns including regions where (1) all groups revealed an increase or decrease of ROH, (2) bison differed from cattle, (3) one cattle breed or groups of breeds differed (e.g., dairy versus meat cattle). Examination of these regions in the cattle genome showed genes potentially important for natural and human-induced selection, concerning, for example, meat and milk quality, metabolism, growth, and immune function. The comparative methodology presented here permits visual identification of regions of interest for selection, breeding programs, and conservation. Cino Pertoldi was supported by a grant from Danish Natural Science Research Council (Grant nos. 11-103926, 09-065999, and 95095995), the Carlsberg Foundation (Grant no. 2011- 01-0059), and the Aalborg Zoo Conservation Foundation (AZCF). Laura Iacolina has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Action (Grant Agreement no. 656697). Astrid V. Stronen received funding from the Danish Natural Science Research Council (Postdoctoral Grant 1337-00007).

The effects of human-caused fragmentation require further study in landscapes where physical dispersal barriers and natural ecological transitions can be discounted as causes for population genetic structure. We predict that fragmentation can reduce dispersal across such barrier-free landscapes because dispersal also is limited by a perception of risk. Considerable fragmentation has occurred in the Riding Mountain National Park (RMNP) region in Manitoba, Canada, during the past 60 years. We examine data from 13 autosomal microsatellites to determine whether fragmentation is correlated with genetic population structure in wolves (Canis lupus). Moderate and significant differentiation between RMNP and a genetic cluster identified 30 km farther north (F ST = 0.053, 95% CI [0.031-0.073]) is consistent with predicted effects of fragmentation. The RMNP population cluster represents at least seven wolf packs followed weekly by radio tracking during 2003-2006. Distinct mtDNA haplotypes have been identified in the Park and no successful wolf dispersal from RMNP has been documented in several multi-year tracking studies since 1974. Tracking data also indicate that some wolves might be reluctant to leave RMNP. Although the influence of behaviour and local adaptation require investigation, human-caused fragmentation appears to have caused cryptic genetic structure on fine spatiotemporal scales in a vagile species that is: (1) not influenced by physical movement barriers or historical ecological discontinuities in our study area, and; (2) able to live relatively close to humans. The Great Plains is now an intensely human-managed landscape. Detection of cryptic genetic structure could therefore function as an important indicator in conservation management.

We examined wolf (Canis lupus) blood and fecal samples from the Riding Mountain National Park (RMNP) region of Manitoba, Canada. In 601 fecal samples collected during two study periods in RMNP and the Duck Mountain Provincial Park and Forest (DMPPF) we found gastrointestinal helminth eggs from Alaria sp. (15.5%), Capillaria sp. (1.0%), taeniid tapeworms (30.8%), Toxascaris sp. (1.7%), Toxocara sp. (0.2%), Trichuris sp. (2.2%), and Moniezia sp. (0.5%). In addition, we found Demodex sp. (0.2%) and the protozoal cysts/oocysts of Sarcocystis sp. (37.3%), Cryptosporidium sp. (1.2%), coccidia (Isospora sp. or Eimeria sp.) (1.7%), and Giardia sp. (29.5%). No fecal shedding of canine parvovirus (CPV, n5387) was detected. All 18 blood samples collected in RMNP showed CPV exposure and eight of 18 blood samples indicated canine distemper virus (CDV) exposure. One wolf died from CDV. Our results are consistent with previous findings on pathogens affecting wolves and with high Giardia sp. prevalence in wolves inhabiting agricultural regions.

Two types of wolves, gray ( Canis lupus L., 1758) and eastern ( Canis lupus lycaon Schreber, 1775 or Canis lycaon ) or Great Lakes wolves, representing Old World (OW) and New World (NW) mitochondrial DNA (mtDNA) haplotypes, have been reported in eastern Canada and the Great Lakes region. Both haplotypes were found in Duck Mountain Provincial Park and Forest, Manitoba. Only OW haplotypes have been reported from the isolated Riding Mountain National Park (RMNP), 30 km to the south. Wolves with NW haplotypes hybridize with C. lupus and coyotes ( Canis latrans Say, 1823) and could mediate gene flow between canids. We examined available data on wolf body mass, skull morphology, and mtDNA from the RMNP region, as well as mtDNA from Manitoba and Saskatchewan, to assess the occurrence of NW haplotypes in wolves and possible canid hybridization. Mean body mass of female (n = 54) and male (n = 42) RMNP wolves during 1985–1987 was higher than that of females (n = 12) and males (n = 8) during 1999–2004. Thirteen skull measures from 29 wolf skulls did not suggest significant differences between RMNP and Duck Mountain wolves. Nineteen of 20 RMNP samples had OW haplotypes, whereas one clustered together with NW haplotypes.

The Norwegian Lundehund breed of dog has undergone a severe loss of genetic diversity as a result of inbreeding and epizootics of canine distemper. As a consequence, the breed is extremely homogeneous and accurate sex identification is not always possible by standard screening of X-chromosomal loci. To improve our genetic understanding of the breed we genotyped 17 individuals using a genome-wide array of 170 000 single nucleotide polymorphisms (SNPs). Standard analyses based on expected homozygosity of X-chromosomal loci failed in assigning individuals to the correct sex, as determined initially by physical examination and confirmed with the Y-chromosomal marker, amelogenin. This demonstrates that identification of sex using standard SNP assays can be erroneous in highly inbred individuals. © The Author 2015; all rights reserved. Published by Oxford University Press on behalf of American Genetic Association. This is the authors' manuscript to the article.

Several mammal species have recolonized their historical ranges across Europe during the last decades. In November 2012, a wolf-looking canid was found dead in Thy National Park (56° 56′ N, 8° 25′ E) in Jutland, Denmark. DNA from this individual and nine German wolves were genotyped using a genome-wide panel of 22,163 canine single nucleotide polymorphism (SNP) markers and compared to existing profiles based on the same marker panel obtained from northeastern Polish (n = 13) wolves, domestic dogs (n = 13) and known wolf-dog hybrids (n = 4). The Thy canid was confirmed to be a wolf from the German-western Polish population, approximately 800 km to the southeast. Access to the German reference database on DNA profiles based on 13 autosomal microsatellites of German wolves made it possible to pinpoint the exact pack origin of the Thy wolf in Saxony, Germany. This was the first documented observation of a wolf in Denmark in 200 years and another example of long-distance dispersal of a carnivore.

Ecological and environmental heterogeneity can produce genetic differentiation in highly mobile species. Accordingly, local adaptation may be expected across comparatively short distances in the presence of marked environmental gradients. Within the European continent, wolves (Canis lupus) exhibit distinct north–south population differentiation. We investigated more than 67‐K single nucleotide polymorphism (SNP) loci for signatures of local adaptation in 59 unrelated wolves from four previously identified population clusters (northcentral Europe n = 32, Carpathian Mountains n = 7, Dinaric‐Balkan n = 9, Ukrainian Steppe n = 11). Our analyses combined identification of outlier loci with findings from genome‐wide association study of individual genomic profiles and 12 environmental variables. We identified 353 candidate SNP loci. We examined the SNP position and neighboring megabase (1 Mb, one million bases) regions in the dog (C. lupus familiaris) genome for genes potentially under selection, including homologue genes in other vertebrates. These regions included functional genes for, for example, temperature regulation that may indicate local adaptation and genes controlling for functions universally important for wolves, including olfaction, hearing, vision, and cognitive functions. We also observed strong outliers not associated with any of the investigated variables, which could suggest selective pressures associated with other unmeasured environmental variables and/or demographic factors. These patterns are further supported by the examination of spatial distributions of the SNPs associated with universally important traits, which typically show marked differences in allele frequencies among population clusters. Accordingly, parallel selection for features important to all wolves may eclipse local environmental selection and implies long‐term separation among population clusters.

Defining biologically relevant seasons is a critical issue in the interpretation of animal space-use studies. Moreover, understanding the effects of extrinsic (e.g., predation risk) and intrinsic (e.g., age and sex) factors on individual differences in seasonal transition dates will deepen our understanding of the mechanisms driving animal movement and potentially population dynamics. We used nonlinear modeling of movement rate over time using global positioning system-collared nonmigratory elk (Cervus elaphus manitobensis) and white-tailed deer (Odocoileus virginianus) in southern Manitoba, Canada, to derive species- and sex-specific seasonal transition dates. In addition, we used variables known to influence timing of migration in migratory populations to explain individual differences in seasonal transition dates. We found ecologically important differences in start and length of seasons between male and female elk and white-tailed deer. Individual differences in seasonal transition dates were large, and could be explained by a combination of intrinsic and extrinsic factors. Age-class of the individual animal and elevation influenced timing of winter, spring, and date of parturition, whereas predation risk from wolves (Canis lupus) influenced onset of spring, summer, and autumn. Our findings suggest that similar extrinsic and intrinsic factors can influence both large- (i.e., migratory) and small-scale movement patterns and can be used effectively to empirically define biologically relevant seasons for sympatric large herbivores.