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The phylum Microsporidia encompasses a diverse group of obligate, intracellular, and spore-forming organisms able to infect a wide range of animal hosts. Among them, Enterocytozoon bieneusi is the most frequently reported species in humans and animals. Little is known about the presence and epidemiology of E. bieneusi in wildlife. We investigated E. bieneusi occurrence and genetic diversity in wild and domestic mammals, through molecular-detection methods, from different regions across Portugal. A total of 756 samples were collected from 288, 242, and 226 wild carnivores, wild ungulates, and domestic animals, respectively. Overall, eight specimens were E. bieneusi-positive (1.1%, 8/756) obtained from five wild (Iberian lynx, Iberian wolf, red fox, stone marten, and wild boar) and one domestic (sheep) host. Nucleotide sequence analysis identified four genotypes of E. bieneusi, Type IV, Wildboar3, BEB6, and PtEbIX. Three of those genotypes belong to Groups 1 (Type IV and Wildboar3) and 2 (BEB6), which are known to contain genotypes capable of infecting a variety of hosts, including humans, highlighting their public health importance. PtEbIX belongs to the dog-specific Group 11. This study represents the first, largest, and most comprehensive molecular-based epidemiology survey carried out in Portugal in wild and domestic animals to date and the first worldwide identification of E. bieneusi in wolf species. Our study showed that wild carnivores and ungulates may act as reservoirs of zoonotic genotypes of E. bieneusi, establishing their role in maintaining the sylvatic cycle of this parasite while representing a potential source of infection for humans and domestic animals.

At the end of the nineteenth century, massive population declines were observed in carnivores due to the emergence of infectious diseases. This study aims to investigate, by means of coprological analysis, the prevalence and intensity of the parasites that infect the endangered Iberian wolf Canis lupus signatus and two mesocarnivores (the red fox Vulpes vulpes and the stone marten Martes foina) in Central Portugal. In total, 67.2% of the samples screened were infected; Toxascaris leonina (40.6%) was the parasite with the highest prevalence, followed by Ancylostomatidae and Eimeria spp. (28.1%). Eimeria spp. was found in stone marten with the highest infection rate (37,800 OPG), followed by T. leonina (10,100 EPG) in a red fox sample. Moderate to high levels of parasitic infections were identified in 73.3% of red foxes from the western area. Our results highlight the possibility of cross-infection among these carnivore species and cross-contamination in the wildlife-livestock-human interface.

espanolLa identificacion de especies mediante tecnicas no invasivas, como la genetica molecular, se ha revelado de importancia en la investigacion ecologica. Durante decadas, la identificacion de excrementos en estudios ecologicos se baso casi exclusivamente en la identificacion morfologica de heces, que a menudo tenian en cuenta la informacion sobre el habitat y la ubicacion del excremento. Sin embargo, este enfoque planteaba serios debates, por la elevada probabilidad de error especifico y por la falta de validacion. El objetivo de este estudio es comprobar el grado de precision a la hora de identificar heces de mesocarnivoros mediante criterios morfologicos, validando estos resultados con la identificacion molecular. Mientras utilizamos solo identificaciones realizadas por expertos para comparar con el estandar de identificacion molecular, tambien comparamos las identificaciones realizadas por observadores con diferentes niveles de experiencia. Se extrajo ADN de 63 heces de mesocarnivoros (NE Portugal), de las cuales fue amplificado y secuenciado con exito el 83% (n= 52) de los extractos: 38 se identificaron molecularmente como de zorro (Vulpes vulpes), ocho como de garduna (Martes foina), dos de marta (Martes martes) y perro domestico (Canis lupus familiaris) y uno de tejon (Meles meles) y gineta (Genetta genetta). Debido al pequeno tamano de la muestra, tan solo fue posible estimar la tasa de error de identificacion de excrementos segun criterios morfologicos (% de veces que las heces fueran mal asignadas a una especie determinada en el campo o en el laboratorio) para zorro y garduna: 4% para muestras de zorro y 62% para las de garduna. La tasa de error cuando se asigno el excremento de una especie a otra en el campo o en el laboratorio (confirmada por tecnicas moleculares) alcanzo el 29% para el zorro (heces identificadas inicialmente como de garduna y de perro) y del 25% para la garduna (heces asignadas a comadreja, Mustela nivalis). Los resultados confirman la conveniencia de incluir metodos moleculares en los estudios ecologicos basados en la identificacion de excrementos, de forma que los investigadores puedan determinar la tasa de error asociada con la discriminacion morfologica para desarrollar estudios de monitoreo mas precisos. espanolSpecies identification of non-invasively collected samples using molecular genetics tools has become an important tool in ecological research. For decades, scat-based ecological studies were almost exclusively rooted in morphological identification of scats, within local context, in the field. However, this approach raised a controversial debate, due to species and context-specific probability of error and lack of validation. In this study, we aimed to test the accuracy of mesocarnivore scats identification, based on morphological criteria, using a carnivore guild in northeastern Portugal as a model and molecular identification as a standard for accuracy of morphological identifications, within local context. While using only expert-based identifications for comparison with molecular identification standard, we have also compared the identifications performed by observers with different levels of experience. We extracted DNA from 63 scats (NE Portugal), which was successfully amplified/sequenced from 83% (n= 52) of the extracts: 38 were molecularly assigned to red fox (Vulpes vulpes), eight to stone marten (Martes foina), two to pine marten (Martes martes) and domestic dog (Canis lupus familiaris) and one to European badger (Meles meles) and common genet (Genetta genetta). There was a tendency for better performance by more experienced researchers, with 67% of scats being correctly assigned, but differences among observers were not significant. Due to the small sample size, only for foxes and stone martens was possible to estimate the error rate in species assignment, based on morphological criteria. False positive rates (% of times a scat was misassigned to a given species) were 4% for fox samples and 62% for stone marten. False negative rates (i.e. the rate at which a scat of a given species was assigned to another species) reached 29% for fox (scats that were initially assigned to stone marten and domestic dog were in fact from fox) and 25% for stone marten (originally misassigned to weasel, Mustela nivalis), respectively. The results support the need to implement molecular methods in ecological studies based on scat identification, so researchers can determine the error rates associated with morphological discrimination to develop accurate monitoring studies.

Habitat loss, due to landscape changes induced by human activities, is considered one of the main drivers of biodiversity decline. Thus, understanding how these changes affect top trophic-level species is essential to develop effective conservation strategy measures to overcome this problem. Mesocarnivores, as higher trophic-level species with crucial roles in ecosystem functioning, are a pivotal functional group in such strategies. Generalist mesocarnivores, such as the red fox (Vulpes vulpes), are excellent models to study species ecological adaption to landscapes moulded by humans. Using generalised linear mixed model (GLMM), we aim to understand how the landscape context affects the presence of this generalist species, in a Mediterranean ecosystem (northeastern Portugal) characterised by a combination of natural areas and traditional agricultural land uses. Based on scats’ distribution, we generated distribution models to test different ecological hypotheses—anthropic disturbance factors, altitude and land-cover patterns. According to our results, red foxes seem to have two distinct strategies: in forest-dominated areas, human activities have a negative effect (disturbance); in areas with a low percentage of forests, agriculture patches and the proximity to urban areas are the main drivers determining its presence, with a positive influence (food availability). Our results confirm the opportunistic character of this species and its high degree of adaptation. Further, the outcome also reveals that landscape context influences the detected pattern. Consequently, considering that populations of the same species are constrained by the same factors, independently of the landscape composition, will affect the effectiveness of management measures that will not account for landscape context effects.

Mammals are threatened worldwide, with ~26% of all species being included in the IUCN threatened categories. This overall pattern is primarily associated with habitat loss or degradation, and human persecution for terrestrial mammals, and pollution, open net fishing, climate change, and prey depletion for marine mammals. Mammals play a key role in maintaining ecosystems functionality and resilience, and therefore information on their distribution is crucial to delineate and support conservation actions. MAMMALS IN PORTUGAL is a publicly available data set compiling unpublished georeferenced occurrence records of 92 terrestrial, volant, and marine mammals in mainland Portugal and archipelagos of the Azores and Madeira that includes 105,026 data entries between 1873 and 2021 (72% of the data occurring in 2000 and 2021). The methods used to collect the data were: live observations/captures (43%), sign surveys (35%), camera trapping (16%), bioacoustics surveys (4%) and radiotracking, and inquiries that represent less than 1% of the records. The data set includes 13 types of records: (1) burrows | soil mounds | tunnel, (2) capture, (3) colony, (4) dead animal | hair | skulls | jaws, (5) genetic confirmation, (6) inquiries, (7) observation of live animal (8), observation in shelters, (9) photo trapping | video, (10) predators diet | pellets | pine cones/nuts, (11) scat | track | ditch, (12) telemetry and (13) vocalization | echolocation. The spatial uncertainty of most records ranges between 0 and 100 m (76%). Rodentia (n=31,573) has the highest number of records followed by Chiroptera (n=18,857), Carnivora (n=18,594), Lagomorpha (n=17,496), Cetartiodactyla (n=11,568) and Eulipotyphla (n=7008). The data set includes records of species classified by the IUCN as threatened (e.g., Oryctolagus cuniculus [n=12,159], Monachus monachus [n=1,512], and Lynx pardinus [n=197]). We believe that this data set may stimulate the publication of other European countries data sets that would certainly contribute to ecology and conservation-related research, and therefore assisting on the development of more accurate and tailored conservation management strategies for each species. There are no copyright restrictions; please cite this data paper when the data are used in publications.

European badgers (Meles meles) are considered central-place foragers, whose spatial ecology is predominantly determined by sett location. Many studies have assessed the factors determining sett site selection throughout this species’ range, but these have often been geographically limited and have primarily identified locally dependent factors. To infer key factors determining sett location, a broader scale approach is needed. Between June 2014 and January 2017, we surveyed mainland Portugal to detect badger setts in 10 × 10 km cells, corresponding to a total of 657.5 km walked line transects. We detected 54 main setts in 136 surveyed cells. Each sett and non-sett site (i.e. transects without setts) was characterised using bioenvironmental variables (e.g. land cover, presence of human infrastructure, soil). We used generalized linear mixed models to test five hypotheses potentially explaining sett location: land cover composition; anthropogenic disturbance; abiotic environmental drivers; trophic resource availability; and a combined effect of all these factors. Our findings show that the key factors for badger sett site selection in Portugal are: (1) disturbance avoidance (low beehive density; absence of livestock; far from hunting reserves), but with a tendency to be located close to highways and unpaved roads; and (2) ease of excavation (avoidance of sedimentary/metamorphic composite rocks). Although specific factors among these drivers may be more important locally or regionally, these major drivers have also been identified elsewhere in Europe. Our nationwide approach contributes to a broader understanding of general patterns of sett site selection by badgers in southern Europe. Furthermore, it provides the national authorities with novel and broad-scale data to facilitate sustainable species conservation of badgers in the southwestern limit of their range.

Human-Induced Rapid Environmental Change (HIREC), particularly climate change and habitat conversion, affects species distributions worldwide. Here, we aimed to (i) assess the factors that determine range patterns of European badger (Meles meles) at the southwestern edge of their distribution and (ii) forecast the possible impacts of future climate and landcover changes on those patterns. We surveyed 272 cells of 5 × 5 km, to assess badger presence and confirmed its occurrence in 95 cells (35%). Our models estimate that badger’s presence is promoted by the occurrence of herbaceous fields and shrublands (5%–10%), and low proportions of Eucalyptus plantations (50% of podzols and eruptive rocks, higher sheep/goat density (>4 ind/km2), an absence of cattle, intermediate precipitation regimes (800–1000 mm/year) and mild mean temperatures (15–16 °C) are also more likely to host badgers. We predict a decrease in favourability of southern areas for hosting badgers under forecasted climate and landcover change scenarios, which may lead to a northwards retraction of the species southern distribution limit, but the overall landscape favourability is predicted to slightly increase. The forecasted retraction may affect community functional integrity, as its role in southern ecological networks will be vacant. Thanks for financial support are due to University of Aveiro (Department of Biology), to CESAM (UID/AMB/50017 - POCI-01-0145-FEDER-007638), to cE3c (UID/BIA/00329/2013), to FCT/MCTES through national funds (PIDDAC), and the co-funding by the FEDER within the PT2020 Partnership Agreement and Compete 2020. JC was supported by a PhD Grant (SFRH/BD/98387/2013) from Fundação para a Ciência e a Tecnologia (FCT), Portugal SI

Mediterranean landscapes in Europe are characterized by a mixed matrix of agriculture, agro-forestry or cattle-farming areas, which have influenced native communities for centuries. Recently, new changes were imposed on these agro-forestry landscapes due to novel management options that provide new challenges for wildlife. From a conservation perspective, there is an urgent need to assess what are the impacts and ecological responses of local wildlife populations to those changes. In the present study, we assessed the influence of human-caused disturbances (e.g. agroforestry practices, cattle-breeding activities and game management), together with food/water and landscape-related factors, on sett site selection by European badgers. We also tested the role of these factors, together with climatic variability, on sett use. We detected that areas further away from water sources, but close to game species feeding structures, have a higher probability of hosting a European badger sett. Moreover, sett use was promoted by low disturbance: setts with lower cattle presence and without understory removal activities were more often in use. Thus, our study shows that, in our study area, agro-forestry and cattle breeding activities constrain badger sett use, while food and water availability influence their distribution. Although badgers have been adapting to anthropogenic activities for centuries, they respond differently depending on the type and intensity of management. Thus, to ensure biodiversity persistence and sustainable human exploitation of the landscape, we need to identify trade-offs between wildlife ecological adaptations and anthropogenic agriculture, forestry and cattle production.

Human–bear conflicts resulting from livestock depredation and crop use are a common threat to the brown bear Ursus arctos throughout its range. Understanding these conflicts requires the recording and categorization of incidents, assessment of their geographical distribution and frequency, and documentation of the financial costs and the presence of any preventative measures. Damage compensation schemes can help mitigate conflicts and, in some cases, improve acceptance of bears. This study aims to elucidate the major factors determining the patterns of damage caused by bears, examine the effectiveness of preventative measures in reducing such damage, and identify bear damage hotspots in Croatia. Our analysis is based on damage reports provided by hunting organizations to the Croatian Ministry of Agriculture during 2004–2014. The highest number of claims were made for damage to field crops and orchards. Damage to livestock, agricultural crops and beehives resulted in the highest total cost to farmers. Damage to beehives and to automatic corn feeders for game species incurred the highest cost per damage event. We identified a hotspot for bear damage claims in Croatia, located near Risnjak National Park and the border with Slovenia. Damage appears higher in areas that have more villages closer to protected areas and a greater per cent of forest cover, indicating a synergistic effect of protected environments that facilitate bear movements and the presence of human activities that provide easily accessible food for bears.

Mediterranean native ecosystems have been disturbed by human activities for millennia and nowadays these landscapes are highly dependent of anthropic management actions which are also responsible for the maintenance of high biodiversity and conservation value. Among the activities that shaped western Mediterranean areas, in particular the “montado” landscapes, agriculture, cattle raising and game activities, have an important role. In this study we aimed to assess if cattle ranching and hunting management might influence European badgers (Meles meles) diet. Results show that badger’s diet is based on the consumption of wheat (Triticum sp.) and insects, whose availability is related with cattle and game management. While wheat is used as supplementary food for game species (e.g. wild rabbit), insects, and especially coprophogous beetles, are associated with cattle dung. This results demonstrate the uses the resources made available by the dominant human activities in the area. No seasonal variation was detected in terms of biomass ingested although the frequency of occurrence of some prey varied along the year, with a higher predation of grasshoppers the dry season, and of crickets, arthropods larvae and acorns in the wet season, a pattern probably related with prey-items availability. We also registered an unusual consumption of mushrooms, also associated with their higher abundance due to climate conditions. This study confirms the opportunistic feeding character of badgers and that in our study area cattle ranching and game activities are being influential in shaping local badger diet.