Mónia Nakamura

Les populations de grands carnivores se sont reconstituées et ont recolonisé plusieurs régions au cours des dernières décennies. Cependant, leur comportement prédateur entraîne souvent des conflits avec l'homme, ce qui se traduit par l'abattage préventif ou en représailles des grands carnivores. La persécution directe et d'autres perturbations anthropogéniques rendent la conservation et la gestion des grands carnivores dans les paysages dominés par l'homme particulièrement difficiles. L'objectif principal de cette thèse est d'étudier l'impact des facteurs anthropogéniques sur la persistance des grands carnivores dans les paysages dominés par l'homme. Parmi tous les grands carnivores, les loups (Canis lupus) sont remarquablement résistants et capables de s'adapter à diverses conditions d'habitat. Les études évaluant la manière dont les facteurs anthropogéniques ou environnementaux affectent la persistance des loups et le nombre d'individus, ainsi que la compréhension de la dynamique et de la démographie des populations de loups, font défaut dans les paysages dominés par l'homme. Basée sur un suivi à long terme des loups dans les paysages ibériques dominés par l'homme, cette thèse estime la répartition spatiale des loups et identifie les zones potentielles de recolonisation ; évalue les caractéristiques des sites de reproduction et identifie les facteurs influençant le nombre d'individus dans les meutes ; et aborde le statut et la viabilité d'une population en évaluant sa dynamique spatio-temporelle, ses paramètres démographiques, et ses probabilités d'extinction.Selon le modèle d'occupation dynamique développé, la probabilité de colonisation des loups était positivement associée à l'altitude, à la densité du bétail et à la densité des routes non asphaltées, et négativement à la proportion de zones brûlées et à la densité des routes nationales-régionales et locales. De manière cohérente, la probabilité d'extinction diminue avec l'augmentation de la densité des routes non asphaltées. En évaluant la dynamique de l'aire de répartition du loup au cours des vingt dernières années en Ibérie, nous avons constaté que les probabilités d'occupation et de colonisation étaient plus élevées dans les zones où les loups ont persisté ou se sont étendus que dans les zones où ils se sont éteints ou à la périphérie de l'aire de répartition de l'espèce. Cependant, les fronts d'expansion inattendus et les stagnations observées au cours des vingt dernières années soulignent l'effet possible des facteurs sociaux liés à l’homme sur le rétablissement des populations de loups et la nécéssité d’evaluer ces facteurs. Sur la base des probabilités de colonisation et d'occupation, une carte d'adéquation de l'habitat a été élaborée, dans laquelle sont identifiées les zones prioritaires pour la mise en œuvre d'actions de conservation et de mesures d'atténuation. En évaluant les caractéristiques autour des sites de reproduction (zones tampons de 1, 2 et 5 km) et les variations du nombre de loups, nous montrons que la disponibilité des refuges influence positivement le nombre d'adultes à toutes les tailles de zones tampons. La densité de la population humaine, la densité des routes asphaltées, la proportion de zones brûlées, la rugosité et la densité des meutes influencent négativement le nombre d'adultes, en particulier dans les zones tampons les plus petites. Bien que les résultats indiquent qu'une plus grande disponibilité de refuges et une plus faible densité de routes non asphaltées augmentent le nombre de jeunes, des recherches supplémentaires sont nécessaires pour évaluer les facteurs qui influencent le nombre de jeunes. Cette étude révèle l'importance des zones avec suffisamment de refuges et peu de perturbations humaines pour le nombre d’individus, en particulier sur les sites de reproduction, car les loups peuvent être particulièrement exposés et sensibles pendant la saison de reproduction.

Cortisol is a biomarker of grey wolf (Canis lupus) prey selection on wild ungulates. Throughout its range, wolves may prey on free-range livestock, leading to conflicts with humans. This can compromise wolf conservation through culling or poaching. We investigate whether glucocorticoid concentration could be a biomarker of individual prey selection by grey wolves that depredate on free-ranging cattle (Bos taurus). To achieve this, cortisol concentration in hair samples from live (n = 46) and wolf-preyed (n = 19) cattle was determined by enzyme-linked immunosorbent assays. The effects of intrinsic and extrinsic variables—namely age, sex and food availability—on hair cortisol concentration (HCC) were investigated through linear mixed models with farm as a random effect. The analysis revealed that, against our initial hypothesis, wolf-preyed cattle had significantly lower HCC than live cattle (P = 0.009). Additionally, HCC was lower in subadults than in adults (P = 0.002), and was negatively correlated with food availability in adults, but not in subadults (P = 0.003). These results suggest that predation risk does not necessarily equal long-term physiological stress. Alternatively, it may indicate that cattle chronically exposed to stressors (i.e. presenting higher HCC) may exhibit more effective anti-predatory behaviours. Additionally, food availability for cattle may influence wolf predation patterns, as cattle may expand their foraging area by exploring unfamiliar areas, thereby increasing the likelihood of predator encounters. Further research is required to understand the relationship between the multitude of stressors acting on free-range cattle and wolf prey selection, with the aim of assessing the risk of individual cattle and eventually managing predation risk and human–wolf conflict.

Animals within social groups respond to costs and benefits of sociality by adjusting the proportion of time they spend in close proximity to other individuals in the group (cohesion). Variation in cohesion between individuals, in turn, shapes important group‐level processes such as subgroup formation and fission–fusion dynamics. Although critical to animal sociality, a comprehensive understanding of the factors influencing cohesion remains a gap in our knowledge of cooperative behavior in animals. We tracked 574 individuals from six species within the genus Canis in 15 countries on four continents with GPS telemetry to estimate the time that pairs of individuals within social groups spent in close proximity and test hypotheses regarding drivers of cohesion. Pairs of social canids (Canis spp.) varied widely in the proportion of time they spent together (5%–100%) during seasonal monitoring periods relative to both intrinsic characteristics and environmental conditions. The majority of our data came from three species of wolves (gray wolves, eastern wolves, and red wolves) and coyotes. For these species, cohesion within social groups was greatest between breeding pairs and varied seasonally as the nature of cooperative activities changed relative to annual life history patterns. Across species, wolves were more cohesive than coyotes. For wolves, pairs were less cohesive in larger groups, and when suitable, small prey was present reflecting the constraints of food resources and intragroup competition on social associations. Pair cohesion in wolves declined with increased anthropogenic modification of the landscape and greater climatic variability, underscoring challenges for conserving social top predators in a changing world. We show that pairwise cohesion in social groups varies strongly both within and across Canis species, as individuals respond to changing ecological context defined by resources, competition, and anthropogenic disturbance. Our work highlights that cohesion is a highly plastic component of animal sociality that holds significant promise for elucidating ecological and evolutionary mechanisms underlying cooperative behavior.

Inbreeding can reduce offspring fitness and has substantial implications for the genetic diversity and long-term viability of populations. In social cooperative canids, inbreeding is conditioned by the geographic proximity between opposite-sex kin outside natal groups and the presence of related individuals in neighbouring groups. Consequently, challenges in moving into other regions where the species is present can also affect inbreeding rates. These can be particularly problematic in areas of high human density, where movement can be restricted, even for highly vagile species. In this study, we investigate the socio-ecological dynamics of Iberian wolf packs in the human-dominated landscape of Alto Minho, in northwest Portugal, where wolves exhibit a high prevalence of short-distance dispersal and limited gene flow with neighbouring regions. We hypothesise that mating occurs regardless of relatedness, resulting in recurrent inbreeding due to high kin encounter rates. Using data from a 10-year non-invasive genetic monitoring programme and a combination of relatedness estimates and genealogical reconstructions, we describe genetic diversity, mate choice, and dispersal strategies among Alto Minho packs. In contrast with expectations, our findings reveal relatedness-based mate choice, low kin encounter rates, and a reduced number of inbreeding events. We observed a high prevalence of philopatry, particularly among female breeders, with the most common breeding strategy involving the pairing of a philopatric female with an unrelated immigrant male. Overall, wolves were not inbred, and temporal changes in genetic diversity were not significant. Our findings are discussed, considering the demographic trend of wolves in Alto Minho and its human-dominated landscape.

Elucidating the evolutionary process of animal adaptation to deserts is key to understanding adaptive responses to climate change. Here we generated 82 individual whole genomes of four fox species (genus Vulpes) inhabiting the Sahara Desert at different evolutionary times. We show that adaptation of new colonizing species to a hot arid environment has probably been facilitated by introgression and trans-species polymorphisms shared with older desert resident species, including a putatively adaptive 25 Mb genomic region. Scans for signatures of selection implicated genes affecting temperature perception, non-renal water loss and heat production in the recent adaptation of North African red foxes (Vulpes vulpes), after divergence from Eurasian populations approximately 78 thousand years ago. In the extreme desert specialists, Rueppell’s fox (V. rueppellii) and fennec (V. zerda), we identified repeated signatures of selection in genes affecting renal water homeostasis supported by gene expression and physiological differences. Our study provides insights into the mechanisms and genetic underpinnings of a natural experiment of repeated adaptation to extreme conditions.

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.

Sarcoptic mange is globally enzootic, and non-invasive methods with high diagnostic specificity for its surveillance in wildlife are lacking. We describe the molecular detection of Sarcoptes scabiei in non-invasively collected faecal samples, targeting the 16S rDNA gene. We applied this method to 843 Iberian wolf Canis lupus signatus faecal samples collected in north-western Portugal (2006–2018). We further integrated this with serological data (61 samples from wolf and 20 from red fox Vulpes vulpes, 1997–2019) in multi-event capture–recapture models. The mean predicted prevalence by the molecular analysis of wolf faecal samples from 2006–2018 was 7.2% (CI₉₅ 5.0–9.4%; range: 2.6–11.7%), highest in 2009. The mean predicted seroprevalence in wolves was 24.5% (CI₉₅ 18.5–30.6%; range: 13.0–55.0%), peaking in 2006–2009. Multi-event capture–recapture models estimated 100% diagnostic specificity and moderate diagnostic sensitivity (30.0%, CI₉₅ 14.0–53.0%) for the molecular method. Mange-infected individually identified wolves showed a tendency for higher mortality versus uninfected wolves (ΔMortality 0.150, CI₉₅ −0.165–0.458). Long-term serology data highlights the endemicity of sarcoptic mange in wild canids but uncovers multi-year epidemics. This study developed and evaluated a novel method for surveying sarcoptic mange in wildlife populations by the molecular detection of S. scabiei in faecal samples, which stands out for its high specificity and non-invasive character.

The physiological significance of biometric body condition indices (bBCI) is poorly understood. We hypothesized that bBCI are composite metrics of nutritional physiology, physical fitness and health. To test this hypothesis, we first compared the performance of eight bBCI, using 434 Southern European carnivores from six species as a model system; and then identified, by non-destructive methods, the hematology and serum biochemistry correlates of three selected bBCI. Fulton’s K Index, Major Axis Regression Residuals and Scaled Mass Index were the only bBCI insensitive to the effect of sex and age. The most informative physiological parameters in explaining the variation of these bBCI were the albumin (Effect Size (ES) = − 1.66 to − 1.76), urea (ES = 1.61 to 1.85) and total bilirubin (ES = − 1.62 to − 1.79). Hemoglobin and globulins (positive) and cholesterol (negative) were moderately informative (0.9 <|ES|< 1.5). This study shows that most bBCI do not control for the effect of age and sex in Southern European carnivores. Our results support that bBCI are composite measures of physiologic processes, reflecting a positive gradient from protein-poor to protein-rich diets, accompanied by increased physical fitness. Biometric body condition indices allow the integration of ecologically relevant physiological aspects in an easily obtained metric.