"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.

The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).

Scavenging patterns of an inbred wolf population in a landscape with a pulse of human-provided carrion.

Scavenging is an important part of food acquisition for many carnivore species that switch between scavenging and predation. In landscapes with anthropogenic impact, humans provide food that scavenging species can utilize. We quantified the magnitude of killing versus scavenging by gray wolves (Canis lupus) in Scandinavia where humans impact the ecosystem through hunter harvest, land use practices, and infrastructure. We investigated the cause of death of different animals utilized by wolves, and examined how the proportion of their consumption time spent scavenging was influenced by season, wolf social affiliation, level of inbreeding, density of moose (Alces alces) as their main prey, density of brown bear (Ursus arctos) as an intraguild competitor, and human density. We used data from 39 GPS-collared wolves covering 3198 study days (2001-2019), including 14,205 feeding locations within space-time clusters, and 1362 carcasses utilized by wolves. Most carcasses were wolf-killed (80.5%) while a small part had died from other natural causes (1.9%). The remaining had either anthropogenic mortality causes (4.7%), or the cause of death was unknown (12.9%). Time spent scavenging was higher during winter than during summer and autumn. Solitary wolves spent more time scavenging than pack-living individuals, likely because individual hunting success is lower than pack success. Scavenging time increased with the mean inbreeding coefficient of the adult wolves, possibly indicating that more inbred individuals resort to scavenging, which requires less body strength. There was weak evidence for competition between wolves and brown bears as well as a positive relationship between human density and time spent scavenging. This study shows how both intrinsic and extrinsic factors drive wolf scavenging behavior, and that despite a high level of inbreeding and access to carrion of anthropogenic origin, wolves mainly utilized their own kills.

Rewilding by Wolf Recolonisation, Consequences for Ungulate Populations and Game Hunting.

The ongoing recolonisations of human-transformed environments in Europe by large carnivores like the wolf Canis lupus means that conservation conflicts could re-surface, among other reasons, due to predation on ungulate game species. We estimated the effect of wolves on ungulate species using data on wolf prey selection, kill rates and territory size to build a hypothetical case of future expansion. We extrapolated results on predation from the current wolf distribution in central Sweden and eastern Poland to the eventual wolf recolonisation of southern Sweden. We then calculated the proportion of five ungulate game species killed annually by wolves, and the ratio between the predicted annual predation by wolves given future colonization and the number of ungulates currently harvested by hunters. Results showed that wolf recolonization in southern Sweden would have a minor impact on the estimated population densities of red deer Cervus elaphus, fallow deer Dama dama and wild boar Sus scrofa, but is likely to lead to a significant reduction in human captures of moose Alces alces and roe deer Capreolus capreolus. The current five-ungulate species system in southern Sweden suggests a potential for two to four times higher wolf density than the two-ungulate species system in the northern part of their current distribution. Management and conservation of recolonizing large carnivores require a better understanding of the observed impact on game populations under similar ecological conditions to ameliorate conservation conflicts and achieve a paradigm of coexistence. Integrating these predictions into management is paramount to the current rewilding trend occurring in many areas of Europe or North America.

Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.

Genetic drift can dramatically change allele frequencies in small populations and lead to reduced levels of genetic diversity, including loss of segregating variants. However, there is a shortage of quantitative studies of how genetic diversity changes over time in natural populations, especially on genome-wide scales. Here, we analyzed whole-genome sequences from 76 wolves of a highly inbred Scandinavian population, founded by only one female and two males, sampled over a period of 30 yr. We obtained chromosome-level haplotypes of all three founders and found that 10%-24% of their diploid genomes had become lost after about 20 yr of inbreeding (which approximately corresponds to five generations). Lost haplotypes spanned large genomic regions, as expected from the amount of recombination during this limited time period. Altogether, 160,000 SNP alleles became lost from the population, which may include adaptive variants as well as wild-type alleles masking recessively deleterious alleles. Although not sampled, we could indirectly infer that the two male founders had megabase-sized runs of homozygosity and that all three founders showed significant haplotype sharing, meaning that there were on average only 4.2 unique haplotypes in the six copies of each autosome that the founders brought into the population. This violates the assumption of unrelated founder haplotypes often made in conservation and management of endangered species. Our study provides a novel view of how whole-genome resequencing of temporally stratified samples can be used to visualize and directly quantify the consequences of genetic drift in a small inbred population.

Multiple species-specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats.

Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA-based methods applied to detect prey in predators' scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species-specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high-throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost-efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.

Behavioral effects of wolf presence on moose habitat selection: testing the landscape of fear hypothesis in an anthropogenic landscape.

Landscape of fear refers to the spatial variation in prey perception of predation risk, that under certain conditions, may lead to changes in their behavior. Behavioral responses of prey in relation to large carnivore predation risk have mainly been conducted in areas with low anthropogenic impact. We used long-term data on the distribution of moose in different habitat types in a system characterized by intensive management of all three trophic levels (silviculture, harvest of wolves and moose) to study effects on moose habitat selection resulting from the return of an apex predator, the wolf. We assumed that coursing predators such as wolves will cause an increased risk for moose in some habitat types and tested the hypotheses that moose will avoid open or young forest habitats following wolf establishment. After wolf recolonization, moose reduced their use of one type of open habitat (bog) but there was neither change in the use of the other open habitat type (clear-cut), nor in their use of young forest. Wolf establishment did not influence the use of habitat close to dense habitat when being in open habitats. Thus, the effect of wolves varied among habitat types and there was no unidirectional support for a behavioral effect of wolves' establishment on moose habitat use. Human-driven habitat heterogeneity, concentration of moose forage to certain habitat types, and the effects of a multiple predator guild on moose may all contribute to the results found. We conclude that the landscape of fear is likely to have weak ecological effects on moose in this system.

Functional traits driving species role in the structure of terrestrial vertebrate scavenger networks.

Species assemblages often have a non-random nested organization, which in vertebrate scavenger (carrion-consuming) assemblages is thought to be driven by facilitation in competitive environments. However, not all scavenger species play the same role in maintaining assemblage structure, as some species are obligate scavengers (i.e., vultures) and others are facultative, scavenging opportunistically. We used a database with 177 vertebrate scavenger species from 53 assemblages in 22 countries across five continents to identify which functional traits of scavenger species are key to maintaining the scavenging network structure. We used network analyses to relate ten traits hypothesized to affect assemblage structure with the "role" of each species in the scavenging assemblage in which it appeared. We characterized the role of a species in terms of both the proportion of monitored carcasses on which that species scavenged, or scavenging breadth (i.e., the species "normalized degree"), and the role of that species in the nested structure of the assemblage (i.e., the species "paired nested degree"), therefore identifying possible facilitative interactions among species. We found that species with high olfactory acuity, social foragers, and obligate scavengers had the widest scavenging breadth. We also found that social foragers had a large paired nested degree in scavenger assemblages, probably because their presence is easier to detect by other species to signal carcass occurrence. Our study highlights differences in the functional roles of scavenger species and can be used to identify key species for targeted conservation to maintain the ecological function of scavenger assemblages.

Age at first reproduction in wolves: different patterns of density dependence for females and males.

Age at first reproduction constitutes a key life-history trait in animals and is evolutionarily shaped by fitness benefits and costs of delayed versus early reproduction. The understanding of how intrinsic and extrinsic changes affects age at first reproduction is crucial for conservation and management of threatened species because of its demographic effects on population growth and generation time. For a period of 40 years in the Scandinavian wolf (Canis lupus) population, including the recolonization phase, we estimated age at first successful reproduction (pup survival to at least three weeks of age) and examined how the variation among individuals was explained by sex, population size (from 1 to 74 packs), primiparous or multiparous origin, reproductive experience of the partner and inbreeding. Median age at first reproduction was 3 years for females (n = 60) and 2 years for males (n = 74), and ranged between 1 and 8-10 years of age (n = 297). Female age at first reproduction decreased with increasing population size, and increased with higher levels of inbreeding. The probability for males to reproduce later first decreased, reaching its minimum when the number of territories approached 40-60, and then increased with increasing population size. Inbreeding for males and reproductive experience of parents and partners for both sexes had overall weak effects on age at first reproduction. These results allow for more accurate parameter estimates when modelling population dynamics for management and conservation of small and vulnerable wolf populations, and show how humans through legal harvest and illegal hunting influence an important life-history trait like age at first reproduction.

Characteristics of reproductive organs and estimates of reproductive potential in Scandinavian male grey wolves (Canis lupus).

Improved knowledge about reproductive patterns and potential in male wolves (i.e., testicular development and size relative to age, pubertal age, and seasonal effects) is needed for evaluation and monitoring of reproductive outcomes in populations. Reproductive organs from 215 male wolves, culled as a result of licensed hunting, protective culling or from carcasses found were examined. The testes and epididymis were weighed and measured. There were biopsy samples collected from the testes and the cauda epididymis for histological determinations if there were spermatozoa in tissues collected. There were reproductive tissue analyses of 197 males while there were separate evaluations of tissues from ten cryptorchid animals. Juvenile wolves (< 1 year, n = 47) had a lesser body mass and mean testes mass than subadult (1-2 years, n = 71) and adult (>2 years, n = 79) males. Season also affected testicular characteristics of structures evaluated with subadult and adult males having a lesser mass during summer months (May-August). Of the 197 males, 70 % had spermatozoa in the seminiferous tubules and the cauda epididymis and were classified as being 'potentially fertile' when tissues were collected, while 22 % were classified as being non-fertile (no spermatozoa, including males that were pre-pubertal) and tissues of 8% could not be evaluated. When testes mass was greater, there was a greater likelihood that spermatozoa were present. There were seven of the ten cryptorchid males of the unilateral type. These testicular and epididymal findings will be useful for evaluating the reproductive potential and management of wolves in Scandinavia.

Impact of a recolonizing, cross-border carnivore population on ungulate harvest in Scandinavia.

Predation from large carnivores and human harvest are the two main mortality factors affecting the dynamics of many ungulate populations. We examined long-term moose (Alces alces) harvest data from two countries that share cross-border populations of wolves (Canis lupus) and their main prey moose. We tested how a spatial gradient of increasing wolf territory density affected moose harvest density and age and sex composition of the harvested animals (n = 549,310), along a latitudinal gradient during 1995-2017. In areas containing average-sized wolf territories, harvest density was on average 37% (Norway) and 51% (Sweden) lower than in areas without wolves. In Sweden, calves made up a higher proportion of the moose harvest than in Norway, and this proportion was reduced with increased wolf territory density, while it increased in Norway. The proportion of females in the adult harvest was more strongly reduced in Sweden than in Norway as a response to increased wolf territory density. Moose management in both countries performed actions aimed to increase productivity in the moose population, in order to compensate for the increased mortality caused by wolves. These management actions are empirical examples of an adaptive management in response to the return of large carnivores.

Wolf habitat selection when sympatric or allopatric with brown bears in Scandinavia.

Habitat selection of animals depends on factors such as food availability, landscape features, and intra- and interspecific interactions. Individuals can show several behavioral responses to reduce competition for habitat, yet the mechanisms that drive them are poorly understood. This is particularly true for large carnivores, whose fine-scale monitoring is logistically complex and expensive. In Scandinavia, the home-range establishment and kill rates of gray wolves (Canis lupus) are affected by the coexistence with brown bears (Ursus arctos). Here, we applied resource selection functions and a multivariate approach to compare wolf habitat selection within home ranges of wolves that were either sympatric or allopatric with bears. Wolves selected for lower altitudes in winter, particularly in the area where bears and wolves are sympatric, where altitude is generally higher than where they are allopatric. Wolves may follow the winter migration of their staple prey, moose (Alces alces), to lower altitudes. Otherwise, we did not find any effect of bear presence on wolf habitat selection, in contrast with our previous studies. Our new results indicate that the manifestation of a specific driver of habitat selection, namely interspecific competition, can vary at different spatial-temporal scales. This is important to understand the structure of ecological communities and the varying mechanisms underlying interspecific interactions.

Scavenging in the Anthropocene: Human impact drives vertebrate scavenger species richness at a global scale.

Understanding the distribution of biodiversity across the Earth is one of the most challenging questions in biology. Much research has been directed at explaining the species latitudinal pattern showing that communities are richer in tropical areas; however, despite decades of research, a general consensus has not yet emerged. In addition, global biodiversity patterns are being rapidly altered by human activities. Here, we aim to describe large-scale patterns of species richness and diversity in terrestrial vertebrate scavenger (carrion-consuming) assemblages, which provide key ecosystem functions and services. We used a worldwide dataset comprising 43 sites, where vertebrate scavenger assemblages were identified using 2,485 carcasses monitored between 1991 and 2018. First, we evaluated how scavenger richness (number of species) and diversity (Shannon diversity index) varied among seasons (cold vs. warm, wet vs. dry). Then, we studied the potential effects of human impact and a set of macroecological variables related to climatic conditions on the scavenger assemblages. Vertebrate scavenger richness ranged from species-poor to species rich assemblages (4-30 species). Both scavenger richness and diversity also showed some seasonal variation. However, in general, climatic variables did not drive latitudinal patterns, as scavenger richness and diversity were not affected by temperature or rainfall. Rainfall seasonality slightly increased the number of species in the community, but its effect was weak. Instead, the human impact index included in our study was the main predictor of scavenger richness. Scavenger assemblages in highly human-impacted areas sustained the smallest number of scavenger species, suggesting human activity may be overriding other macroecological processes in shaping scavenger communities. Our results highlight the effect of human impact at a global scale. As species-rich assemblages tend to be more functional, we warn about possible reductions in ecosystem functions and the services provided by scavengers in human-dominated landscapes in the Anthropocene.

Testing the influence of habitat experienced during the natal phase on habitat selection later in life in Scandinavian wolves.

Natal habitat preference induction (NHPI) occurs when characteristics of the natal habitat influence the future habitat selection of an animal. However, the influence of NHPI after the dispersal phase has received remarkably little attention. We tested whether exposure to humans in the natal habitat helps understand why some adult wolves Canis lupus may approach human settlements more than other conspecifics, a question of both ecological and management interest. We quantified habitat selection patterns within home ranges using resource selection functions and GPS data from 21 wolf pairs in Scandinavia. We identified the natal territory of each wolf with genetic parental assignment, and we used human-related characteristics within the natal territory to estimate the degree of anthropogenic influence in the early life of each wolf. When the female of the adult wolf pair was born in an area with a high degree of anthropogenic influence, the wolf pair tended to select areas further away from humans, compared to wolf pairs from natal territories with a low degree of anthropogenic influence. Yet the pattern was statistically weak, we suggest that our methodological approach can be useful in other systems to better understand NHPI and to inform management  about human-wildlife interactions.

Data to model risks for recolonizing wolves in Scandinavia through the integration of territory presence and human-driven mortalities.

This dataset article describes the data and sources used to model risks for the recolonizing wolf (Canis lupus) in Sweden and Norway in the article "Integrated spatially-explicit models predict pervasive risks to recolonizing wolves in Scandinavia from human-driven mortality" (Recio et al., 2018). Presences on wolf territories were used to model the potential distribution of the species. Presences of human-driven mortalities including traffic collisions, culling (protective/defensive, and licensed hunting), and illegal killing (i.e. poaching) were used to model predictions on the distribution of these mortalities. Sources for the independent variables used for the models are also described.

No place like home? A test of the natal habitat-biased dispersal hypothesis in Scandinavian wolves.

Natal dispersal is an important mechanism for the viability of populations. The influence of local conditions or experience gained in the natal habitat could improve fitness if dispersing individuals settle in an area with similar habitat characteristics. This process, defined as 'natal habitat-biased dispersal' (NHBD), has been used to explain distribution patterns in large carnivores, but actual studies evaluating it are rare. We tested whether grey wolf Canis lupus territory establishment was influenced by the habitat characteristics of the natal territory using the long-term monitoring of the Scandinavian wolf population. We paired the locations of natal and established territories, accounted for available habitats along the dispersing route, and compared their habitat characteristics for 271 wolves during 1998-2012. Wolves with the shortest dispersal distances established in natal-like habitat types more than expected by chance, whereas wolves that dispersed longer distances did not show NHBD. The pattern was consistent for male and female wolves, with females showing more NHBD than males. Chances to detect NHBD increased with the size of habitat defined as available. This highlights the importance of considering the biological characteristics of the studied species when defining habitat availability. Our methodological approach can prove useful to inform conservation and management to identify habitats to be selected by reintroduced or naturally expanding populations.

Habitat segregation between brown bears and gray wolves in a human-dominated landscape.

Identifying how sympatric species belonging to the same guild coexist is a major question of community ecology and conservation. Habitat segregation between two species might help reduce the effects of interspecific competition and apex predators are of special interest in this context, because their interactions can have consequences for lower trophic levels. However, habitat segregation between sympatric large carnivores has seldom been studied. Based on monitoring of 53 brown bears (Ursus arctos) and seven sympatric adult gray wolves (Canis lupus) equipped with GPS collars in Sweden, we analyzed the degree of interspecific segregation in habitat selection within their home ranges in both late winter and spring, when their diets overlap the most. We used the K-select method, a multivariate approach that relies on the concept of ecological niche, and randomization methods to quantify habitat segregation between bears and wolves. Habitat segregation between bears and wolves was greater than expected by chance. Wolves tended to select for moose occurrence, young forests, and rugged terrain more than bears, which likely reflects the different requirements of an omnivore (bear) and an obligate carnivore (wolf). However, both species generally avoided human-related habitats during daytime. Disentangling the mechanisms that can drive interspecific interactions at different spatial scales is essential for understanding how sympatric large carnivores occur and coexist in human-dominated landscapes, and how coexistence may affect lower trophic levels. The individual variation in habitat selection detected in our study may be a relevant mechanism to overcome intraguild competition and facilitate coexistence.

Genomic consequences of intensive inbreeding in an isolated wolf population.

Inbreeding (mating between relatives) is a major concern for conservation as it decreases individual fitness and can increase the risk of population extinction. We used whole-genome resequencing of 97 grey wolves (Canis lupus) from the highly inbred Scandinavian wolf population to identify 'identical-by-descent' (IBD) chromosome segments as runs of homozygosity (ROH). This gave the high resolution required to precisely measure realized inbreeding as the IBD fraction of the genome in ROH (F ROH). We found a striking pattern of complete or near-complete homozygosity of entire chromosomes in many individuals. The majority of individual inbreeding was due to long IBD segments (>5 cM) originating from ancestors ≤10 generations ago, with 10 genomic regions showing very few ROH and forming candidate regions for containing loci contributing strongly to inbreeding depression. Inbreeding estimated with an extensive pedigree (F P) was strongly correlated with realized inbreeding measured with the entire genome (r 2 = 0.86). However, inbreeding measured with the whole genome was more strongly correlated with multi-locus heterozygosity estimated with as few as 500 single nucleotide polymorphisms, and with F ROH estimated with as few as 10,000 single nucleotide polymorphisms, than with F P. These results document in fine detail the genomic consequences of intensive inbreeding in a population of conservation concern.

Fear or food - abundance of red fox in relation to occurrence of lynx and wolf.

Apex predators may affect mesopredators through intraguild predation and/or supply of carrion from their prey, causing a trade-off between avoidance and attractiveness. We used wildlife triangle snow-tracking data to investigate the abundance of red fox (Vulpes vulpes) in relation to lynx (Lynx lynx) and wolf (Canis lupus) occurrence as well as land composition and vole (Microtus spp.) density. Data from the Swedish wolf-monitoring system and VHF/GPS-collared wolves were used to study the effect of wolf pack size and time since wolf territory establishment on fox abundance. Bottom-up processes were more influential than top-down effects as the proportion of arable land was the key indicator of fox abundance at the landscape level. At this spatial scale, there was no effect of wolf abundance on fox abundance, whereas lynx abundance had a positive effect. In contrast, at the wolf territory level there was a negative effect of wolves on fox abundance when including detailed information of pack size and time since territory establishment, whereas there was no effect of lynx abundance. This study shows that different apex predator species may affect mesopredator abundance in different ways and that the results may be dependent on the spatiotemporal scale and resolution of the data.

Mesopredator behavioral response to olfactory signals of an apex predator.

Olfactory signals constitute an important mechanism in interspecific interactions, but little is known regarding their role in communication between predator species. We analyzed the behavioral responses of a mesopredator, the red fox (Vulpes vulpes), to an olfactory cue (scat) of an apex predator, the lynx (Lynx lynx) in Bialowieza Primeval Forest, Poland, using video camera traps. Red fox visited sites with scats more often than expected and the duration of their visits was longer at scat sites than at control sites (no scat added). Vigilant behavior, sniffing and scent marking (including over-marking) occurred more often at scat sites compared to control sites, where foxes mainly passed by. Vigilance was most pronounced during the first days of the recordings. Red fox behavior was also influenced by foxes previously visiting scat sites. They sniffed and scent marked (multiple over-marking) more frequently when the lynx scat had been over-marked previously by red fox. Fox visits to lynx scats may be seen as a trade-off between obtaining information on a potential food source (prey killed by lynx) and the potential risk of predation by an apex predator.