Projection of current and future distribution of adaptive genetic units in an alpine ungulate.

Climate projections predict major changes in alpine environments by the end of the 21st century. To avoid climate-induced maladaptation and extinction, many animal populations will either need to move to more suitable habitats or adapt in situ to novel conditions. Since populations of a species exhibit genetic variation related to local adaptation, it is important to incorporate this variation into predictive models to help assess the ability of the species to survive climate change. Here, we evaluate how the adaptive genetic variation of a mountain ungulate-the Northern chamois (Rupicapra rupicapra)-could be impacted by future global warming. Based on genotype-environment association analyses of 429 chamois using a ddRAD sequencing approach, we identified genetic variation associated with climatic gradients across the European Alps. We then delineated adaptive genetic units and projected the optimal distribution of these adaptive groups in the future. Our results suggest the presence of local adaptation to climate in Northern chamois with similar genetic adaptive responses in geographically distant but climatically similar populations. Furthermore, our results predict that future climatic changes will modify the Northern chamois adaptive landscape considerably, with various degrees of maladaptation risk.

Age-specific survival of territorial and non-territorial male chamois.

How alternative reproductive tactics (ARTs) are maintained in wildlife populations is one of the major questions in evolutionary biology. As a dominant status, territoriality is typically linked to increased mating opportunities, and one explanation why this behaviour coexists with other tactics is that dominance implies survival costs. Such a trade-off may occur in the Northern chamois Rupicapra rupicapra, as reproductive advantages of territorial males over non-territorial males could be counterbalanced by a reduction in survival mediated through energy expenditure, stress and parasitic infections, ultimately favouring ART coexistence. Here, we analysed age-dependent survival probabilities of territorial (n = 15) and non-territorial (n = 16) adult chamois using information collected over 12 years between 2010 and 2021 in the Gran Paradiso National Park (Western Italian Alps). Survival rates were estimated with a CMR approach using Burnham's joint modelling of live encounter and dead recovery data. The model selection procedure, based on AICc value minimisation, supported a linear decrease of survival with age but the results did not match our predictions, as territorial chamois did not have lower survival rates than non-territorial chamois. In contrast, territorial males appeared to enjoy reproductive success at lower survival costs. This, in turn, supports the role of other factors, such as snow-dependent environmental stochasticity, in the maintenance of ARTs in chamois populations. The limited sample size, however, calls for caution in interpretation, and long-term studies of lifetime reproductive success and survival are necessary to clarify the mechanisms underlying the expression and coexistence of different reproductive behaviours in this species.

Parasite-mediated manipulation? Toxoplasma gondii infection increases risk behaviour towards culling in red deer.

Parasites can modify host behaviour to increase their chances of survival and transmission. Toxoplasma gondii is a globally distributed protozoan whose ability to modify host behaviour is well known in taxa such as rats and humans. Less well known are the effects on the behaviour of wild species, with the exception of a few studies on primates and carnivores. Taking advantage of a culling activity conducted in Stelvio National Park (Italy), the serological status of T. gondii was studied in 260 individuals of red deer Cervus elaphus with respect to the risk of being culled. A temporal culling rank index was fitted as a response variable, and T. gondii serological status as the main explanatory variable in linear models, accounting for covariates such as sex, age, jaw length, bone marrow fat and culling location. The overall seroprevalence of T. gondii was 31.5%, and the selected models suggested that seropositive deer were culled earlier than seronegative ones, but this effect was only evident in females, in individuals with medium-good body condition, and in areas with greater human presence. Our results suggest that T. gondii may be involved in risk behaviour in large herbivores, supporting its role as a facilitator of predation risk.

Molecular characterization of Dictyocaulus nematodes in wild red deer Cervus elaphus in two areas of the Italian Alps.

Nematodes of the genus Dictyocaulus are the causative agents of parasitic bronchitis and pneumonia in several domestic and wild ungulates. Various species have been described in wild cervids, as the case of Dictyocaulus cervi in red deer, recently described as a separate species from Dictyocaulus eckerti. In Italy, information on dictyocaulosis in wildlife is limited and often outdated. In this work, 250 red deer were examined for the presence of Dictyocaulus spp. in two areas of the Italian Alps (n = 104 from Valle d'Aosta, n = 146 from Stelvio National Park), and the retrieved lungworms were molecularly characterized. Lungworms were identified in 23 and 32 animals from Valle d'Aosta and Stelvio National Park, respectively. The nematodes, morphologically identified as D. cervi, were characterized molecularly (18S rDNA, ITS2, and coxI). Consistently, almost all specimens were found to be phylogenetically related to D. cervi. Three individuals, detected from both study sites and assigned to an undescribed Dictyocaulus sp., clustered with Dictyocaulus specimens isolated from red deer and fallow deer in previous studies. Within each of D. cervi and the undescribed Dictyocaulus sp., the newly isolated nematodes phylogenetically clustered based on their geographical origin. This study revealed the presence of D. cervi in Italian red deer, and an undetermined Dictyocaulus sp. that should be more deeply investigated. The results suggest that further analyses should be focused on population genetics of cervids and their lungworms to assess how they evolved, or co-evolved, throughout time and space and to assess the potential of transmission towards farmed animals.

Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.

A scientifically informed approach to decision-making is key to ensuring the sustainable management of ecosystems, especially in the light of increasing human pressure on habitats and species. Protected areas, with their long-term institutional mandate for biodiversity conservation, play an important role as data providers, for example, through the long-term monitoring of natural resources. However, poor data management often limits the use and reuse of this wealth of information. In this paper, we share lessons learned in managing long-term data from the Italian Alpine national parks. Our analysis and examples focus on specific issues faced by managers of protected areas, which partially differ from those faced by academic researchers, predominantly owing to different mission, governance, and temporal perspectives. Rigorous data quality control, the use of appropriate data management tools, and acquisition of the necessary skills remain the main obstacles. Common protocols for data collection offer great opportunities for the future, and complete recovery and documentation of time series is an urgent priority. Notably, before data can be shared, protected areas should improve their data management systems, a task that can be achieved only with adequate resources and a long-term vision. We suggest strategies that protected areas, funding agencies, and the scientific community can embrace to address these problems. The added value of our work lies in promoting engagement with managers of protected areas and in reporting and analysing their concrete requirements and problems, thereby contributing to the ongoing discussion on data management and sharing through a bottom-up approach.

Temporal stability of fecal cortisol metabolites in mountain-dwelling ungulates.

Fecal cortisol metabolites (FCMs) are widely used to track stress responses in wildlife and captive species. Rules of thumb suggest that samples should be collected as soon as possible after defecation, to avoid decay of FCMs. To date, however, only a few studies investigated the stability of defecated FCMs over time, and most of them were conducted in controlled laboratory conditions. Here, we investigated the stability of FCMs over seven consecutive days, in two mountain-dwelling ungulates, under natural environmental conditions using a semi-experimental approach. Fecal samples from Northern chamois Rupicapra rupicapra (n = 24) and red deer Cervus elaphus (n = 22) were collected in summer of 2020 within the Stelvio National Park, Italy, and placed in an open area above 2000 m a.s.l. For the next 7 days, we collected a portion of each sample, and all sub-samples were analyzed with an 11-oxoetiocholanolone enzyme immunoassay. Exposure, temperature, and precipitation were fitted as covariates in non-linear generalized mixed models to assess FCM variation over time, and competing models were selected using AICc. For chamois, the best model included only time as a predictor, while for red deer, it included time, precipitation, and exposure. For both species, FCM values decreased rapidly from the first days after deposition until the fourth day. For red deer, in northern-exposed samples, FCM values decreased slower than in south-exposed ones; furthermore, FCM values increased with increasing precipitation. Our results offer a solid methodological basis to wildlife researchers and practitioners interested in the investigation of the ecological factors affecting stress variation in wildlife and support the recommendation to collect samples as fresh as possible, to avoid misleading inference. Further studies are necessary to evaluate the stability of FCMs when other enzyme immunoassays are used.

Forests buffer the climate-induced decline of body mass in a mountain herbivore.

Climate change is known to affect key life-history traits, such as body mass, reproduction, and survival in many species. Animal populations inhabiting mountain habitats are adapted to extreme seasonal environmental conditions but are also expected to be especially vulnerable to climate change. Studies on mountain ungulates typically focus on populations or sections of populations living above the tree line, whereas populations inhabiting forested habitats are largely understudied. Here, we investigate whether forested areas can mitigate the impact of climatic change on life-history traits by evaluating the interactive effects of temperature and habitat characteristics on body mass variation in the Alpine chamois Rupicapra rupicapra rupicapra. We examined data of 20,573 yearling chamois collected from 1993 to 2019 in 28 mountain ranges in the Austrian Eastern Alps, characterized by different proportion of forest cover. Our results show that the temporal decline of chamois body mass is less pronounced in areas with greater proportion of forest cover. For chamois living in forest habitats only, no significant temporal change in body mass was detected. Variation in body mass was affected by the interaction between density and snow cover, as well as by the interaction between spring temperatures and forest cover, supporting the role of forests as thermal buffer against the effects of increasing temperatures on life-history traits in a mountain ungulate. In turn, this study suggests a buffering effect of forests against climate change impacts. Assessments of the consequences of climate change on the life-history traits and population dynamics of mountain-dwelling species should thus consider the plasticity of the species with respect to the use and availability of different habitat types.

Unravelling the sex- and age-specific impact of poaching mortality with multievent modeling.

BACKGROUND: Poaching is a prominent source of 'hidden hurdles', cryptic impacts of human activities that may hinder the conservation of animal populations. Estimating poaching mortality is challenging, as the evidence for illegal killing is not outwardly obvious. Using resighting and recovery data collected on 141 marked red deer Cervus elaphus within the Stelvio National Park (central Italian Alps), we show how multievent models allow to assess the direct impacts of illegal harvesting on age- and sex-specific survival, accounting for uncertainty over mortality causes. RESULTS: Mortality caused by poaching was consistently higher for males than for females in all age classes. In males, the probability of dying from poaching was higher for extreme age classes, while in females all age classes showed fairly similar values of poaching mortality. The strong bias in sex-specific poaching mortality was possibly due to trophy killing in adult males and 'bushmeat-like' killing for private or commercial gain in young males and in females. CONCLUSIONS: A robust assessment of age- and sex-specific prevalence of poaching in wildlife populations is pivotal when illegal killing is of conservation concern. This provides timely information on what segment of the population is most likely to be affected. Besides obvious demographic consequences on small populations, age- and sex-biased poaching prevalence may contrast with the need to maintain ecosystem complexity and may alter behavioral responses to human presence. The information provided by multievent models, whose flexibility makes them adaptable to many systems where individual-based data is part of population monitoring, offers a support to design appropriate strategies for the conservation of wildlife populations.

Physiological response to etho-ecological stressors in male Alpine chamois: timescale matters!

From a life history perspective, glucocorticoids secreted by the neuroendocrine system, integrating different sources of stress through an adaptive feedback mechanism, may have important consequences on individual fitness. Although stress responses have been the object of several investigations, few studies have explored the role of proximate mechanisms responsible for the potential trade-offs between physiological stress and life history traits integrating social and environmental stressors. In 2011 and 2012, we collected data on faecal cortisol metabolites (FCM) in a marked male population of Alpine chamois, within the Gran Paradiso National Park (Italy). Using a model selection approach we analysed the effect of potential etho-ecological stressors such as age, social status (territorial vs. non-territorial males), minimum temperature, snow depth and precipitation on FCM variation. To correctly interpret environmentally and socially induced stress responses, we conducted model selections over multiple temporal scales defined a priori: year, cold months, spring, warm months, mating season. Over the year, FCM levels showed a negative relationship with minimum temperature, but altogether, climatic stressors had negligible effects on glucocorticoid secretion, possibly owing to good adaptations of chamois to severe weather conditions. Age was negatively related to FCM during the rut, possibly due to greater experience of older males in agonistic contests. Social status was an important determinant of FCM excretion: while both the 'stress of subordination' and the 'stress of domination' hypotheses received some support in spring and during the mating season, respectively, previous data suggest that only the latter may have detrimental fitness consequences on male chamois.

The Alpine ibex (Capra ibex) gut microbiome, seasonal dynamics, and potential application in lignocellulose bioconversion.

Aiming to shed light on the biology of wild ruminants, we investigated the gut microbiome seasonal dynamics of the Alpine ibex (Capra ibex) from the Central Italian Alps. Feces were collected in spring, summer, and autumn during non-invasive sampling campaigns. Samples were analyzed by 16S rRNA amplicon sequencing, shotgun metagenomics, as well as targeted and untargeted metabolomics. Our findings revealed season-specific compositional and functional profiles of the ibex gut microbiome that may allow the host to adapt to seasonal changes in available forage, by fine-tuning the holobiont catabolic layout to fully exploit the available food. Besides confirming the importance of the host-associated microbiome in providing the phenotypic plasticity needed to buffer dietary changes, we obtained species-level genome bins and identified minimal gut microbiome community modules of 11-14 interacting strains as a possible microbiome-based solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids.

Active surveillance of paratuberculosis in Alpine-dwelling red deer (Cervus elaphus).

Paratuberculosis (Johne's disease) is a globally widespread infectious disease affecting domestic and wild ruminants, caused by Mycobacterium avium subsp. paratuberculosis (MAP). The bacterium is excreted in the feces and is characterized by high environmental resistance. The new Animal Health Law (Regulation EU 2016/429) on transmissible animal diseases, recently in force throughout the European Union, includes paratuberculosis within the diseases requiring surveillance in the EU, listing some domestic and wild Bovidae, Cervidae, and Camelidae as potential reservoirs. Taking advantage of a culling activity conducted in the Stelvio National Park (Italy), this study investigated MAP infection status of red deer (Cervus elaphus) between 2018 and 2022, and evaluated the probability of being MAP-positive with respect to individual and sampling-level variables. A total of 390 subjects were examined macroscopically and tested for MAP, using different diagnostic tools: IS900 qPCR, culture, histopathology, and serology. Twenty-three of them were found positive for MAP by at least one test, with an overall prevalence of 5.9% (95% CI 4.0-8.7), that, respectively, ranged from 12.4% in the first culling season to 2.0 and 2.1% in the 2019-2020 and 2021-2022 culling seasons. Quantitative PCR assay on ileocecal valve and mesenteric lymph nodes detected the highest number of MAP positive animals. The results of the study showed the increased probability of being MAP-positive with increasing age and that red deer with lower body mass values were more likely to be infected with MAP. Overall, the absence of signs of clinical paratuberculosis and gross lesions together with the low level of shedding witness early phases of the disease among the positive red deer and support an improvement of the paratuberculosis status of this population, as shown by the decreased prevalence of the disease over the years.

Season-dependent impact of forage quality on stress in alpine chamois.

Chronically heightened stress levels in wildlife species may have detrimental effects on individual life history traits, for example, through the increased likelihood of disease, parasitic infections, and overall reduced fitness. Understanding the drivers of stress may thus have great potential for informing wildlife conservation. Although the role of climate and individual status is well studied in stress ecology, the impact of related stressors such as dietary quality is of increasing interest to wildlife research and conservation. In this study, fecal cortisol metabolites (FCMs) in Alpine chamois Rupicapra r. rupicapra used as bioindicators of stress, and their relationship with forage quality-measured as the percentage of fecal crude protein (CP)-were investigated. Data collection took place in 2011 and 2012 in the Gran Paradiso National Park (Western Italian Alps), on 22 individually marked adult males. The relationship between FCMs and CPs was analyzed through linear models and separated between winter and summer months, accounting for the effect of potentially confounding exogenous and endogenous variables. After AICc-based model selection, we found that forage quality was negatively related to FCM levels in Alpine chamois during the summer months, meaning that higher quality forage was associated with the decreased expression of stress hormones. However, during the winter months, we did not find a significant relationship, potentially as a result of forage quality being ubiquitously poor. Although the mechanisms through which dietary variations impact FCM concentrations in wildlife populations are largely unknown, the occurrence of significant relationships between forage quality and stress levels supports potentially important implications for the long-term effect of climatic changes on the fitness of wildlife populations.

Habitat and climate shape growth patterns in a mountain ungulate.

Uptake and use of energy are of key importance for animals living in temperate environments that undergo strong seasonal changes in forage quality and quantity. In ungulates, energy intake strongly affects body mass gain, an important component of individual fitness. Energy allocation among life-history traits can be affected by internal and external factors. Here, we investigate large-scale variation in body growth patterns of Alpine chamois Rupicapra rupicapra rupicapra, in relation to sex, age, temperature, and habitat variations across 31 (sub)populations in the Central European Alps. Taking advantage of an exceptionally large dataset (n = 178,175) of chamois hunted over 27 consecutive years between 1993 and 2019 in mountain ranges with different proportions of forest cover, we found that (i) patterns of body mass growth differ between mountain ranges, with lower body mass but faster mass growth with increasing proportion of forest cover and that (ii) the effect of spring and summer temperatures on changes in body growth patterns are larger in mountain ranges with lower forest cover compared to mountain ranges with higher forest cover. Our results show that patterns of body mass growth within a species are more plastic than expected and depend on environmental and climatic conditions. The recent decline in body mass observed in Alpine chamois populations may have greater impacts on populations living above the treeline than in forests, which may buffer against the effects of increasing temperatures on life-history traits.

Survey of Staphylococcus aureus carriage by free-living red deer (Cervus elaphus): Evidence of human and domestic animal lineages.

Staphylococcus aureus is a pathogen that can affect multiple host species. Evidence of transmission between humans and animals and among different animal species has been reported in recent years. In this study, we investigated 284 free-living red deer (Cervus elaphus) in the Central Italian Alps to assess the prevalence and molecular characteristics of S. aureus in nasal and intestinal samples in relation to host features and environmental factors. A prevalence of 90%, 26.2% and 10.7% of S. aureus was detected in nasal rectal swabs and faeces, respectively. Calves had a higher probability of being S. aureus intestinal carriers than adults, especially in females when considering faecal samples. Clonal complex (CC) 425 was the most prevalent lineage (61.5%). This is a lineage known to be widespread in both domestic and free-living animals. It was followed by CC2671 (15.4%) and CC350 (6.4%). A high rate of the phage-borne virulence factor lukM/lukF-P83 was detected in CC425 and CC350. Further lineages, which are known to occur in both humans and animals, were detected sporadically in red deer faeces only, that is, CC7, CC9, CC121 and CC707, harbouring the genes of the penicillinase operon and a gene for macrolide resistance (CC9 and CC121). Methicillin resistance genes mecA and mecC were not found. Our results suggest that free-living red deer may be reservoir for S. aureus in Alpine habitats.

Free-ranging red deer (Cervus elaphus) as carriers of potentially zoonotic Shiga toxin-producing Escherichia coli.

Shiga toxin-producing E. coli (STEC) are zoonotic foodborne pathogens of outmost importance and interest has been raised in recent years to define the potential zoonotic role of wildlife in STEC infection. This study aimed to estimate prevalence of STEC in free-ranging red deer (Cervus elaphus) living in areas with different anthropisation levels and describe the characteristics of strains in order to evaluate the potential risk posed to humans. Two-hundred one deer faecal samples collected in 2016-2018 from animals of Central Italian Alps were examined by bacteriological analysis and PCR screening of E. coli colonies for stx1, stx2 and eae genes. STEC strains were detected in 40 (19.9%) deer, with significantly higher prevalence in offspring than in yearlings. Whole genome analysis was performed to characterise a subset of 31 STEC strains. The most frequently detected serotype was O146:H28 (n = 10, 32.3%). Virulotyping showed different stx subtypes combinations, with stx2b-only (n = 15, 48.4%) being the most prevalent. All STEC lacked the eae gene but harbored additional virulence genes, particularly adhesins, toxins and/or other colonisation factors also described in STEC isolated from disease in humans. The most frequently detected genes were astA (n = 22, 71%), subAB (n = 21, 68%), iha (n = 26, 83.9%) and lpfA (n = 24, 77%). Four hybrid STEC/Enterotoxigenic E. coli strains were also identified. According to the most recent paradigm for pathogenicity assessment of STEC issued by the European Food Safety Authority, our results suggest that red deer are carriers of STEC strains that may have zoonotic potential, regardless of the anthropisation levels. Particular attention should be drawn to these findings while handling and preparing game meat. Furthermore, deer may release STEC in the environment, possibly leading to the contamination of soil and water sources.

Regression Models, Fantastic Beasts, and Where to Find Them: A Simple Tutorial for Ecologists Using R.

Regression modeling is a workhorse of statistical ecology that allows to find relationships between a response variable and a set of explanatory variables. Despite being one of the fundamental statistical ideas in ecological curricula, regression modeling can be complex and subtle. This paper is intended as an applied protocol to help students understand the data, select the most appropriate models, verify assumptions, and interpret the output. Basic ecological questions are tackled using data from a fictional series, "Fantastic beasts and where to find them," with the aim to show how statistical thinking can foster curiosity, creativity and imagination in ecology, from the formulation of hypotheses to the interpretation of results.

Spatial variation in antler investment of Apennine red deer.

Heterogeneity in resource availability and quality can trigger spatial patterns in the expression of sexually selected traits such as body mass and weaponry. While relationships between habitat features and phenotypic quality are well established at broad geographical scales, information is poor on spatial patterns at finer, intrapopulation scales. We analyzed biometric data collected on 1965 red deer Cervus elaphus males over 20 years from a nonmigratory population living on two sides of a mountainous ridge, with substantial differences in land cover and habitat quality but similar climate and population density. We investigate spatial patterns in (i) body mass, (ii) antler mass, and (iii) antler investment. We also tested for site- and age-specific patterns in allometric relationship between body mass and antler mass. Statistically significant fine-scale spatial variations in body mass, antler mass, and, to a lesser extent, antler allocation matched spatial differences in land cover. All three traits were greater in the northern slope, characterized by higher habitat heterogeneity and greater availability of open habitats, than in the southern slope. Moreover, the allometric relationship between body mass and antler mass differed among age-classes, in a pattern that was consistent between the two mountain slopes. Our results support the occurrence of spatial patterns in the expression of individual attributes also at a fine, intrapopulation scale. Our findings emphasize the role of environmental heterogeneity in shaping spatial variations of key life-history traits, with potential consequences for reproductive success.

Disentangling demographic effects of red deer on chamois population dynamics.

Investigating the impact of ecological factors on sex- and age-specific vital rates is essential to understand animal population dynamics and detect the potential for interactions between sympatric species. We used block count data and autoregressive linear models to investigate variation in birth rate, kid survival, female survival, and male survival in a population of Alpine chamois Rupicapra rupicapra rupicapra monitored over 27 years within the Stelvio National Park, Central Italian Alps, as function of climatic variables, density dependence, and interspecific competition with red deer Cervus elaphus. We also used path analysis to assess the indirect effect of deer abundance on chamois growth rate mediated by each demographic parameter. Based on previous findings, we predicted that birth rate at [t] would negatively relate to red deer abundance at year [t - 1]; survival rates between [t] and [t + 1] would negatively relate to red deer abundance at year [t - 1] and to the interactive effect of winter precipitation at [t + 1] and chamois density at [t]. Our results showed that birth rate was positively related to spring-summer precipitation in the previous year, but this effect was hampered by increasing red deer abundance. Kid and female survival rates were negatively related to the combined effect of chamois abundance and winter precipitation. Male and female survival rates were negatively related to lagged red deer abundance. The path analysis supported a negative indirect effect of red deer abundance on chamois growth rate mediated by birth rate and female survival. Our results suggest that chamois population dynamics was largely explained by the synergistic effect of density dependence and winter harshness, as well as by interspecific competition with red deer, whose effects were seemingly stronger on the kid-female segment of the population.

Linking alternative reproductive tactics and habitat selection in Northern chamois.

In polygynous ungulates, males may achieve fertilization through the use of alternative reproductive tactics (ARTs), discrete phenotypic variations evolved to maximize fitness. ARTs are often associated with different male spatial strategies during the rut, from territoriality to female-following. Although variation in space use patterns of rutting male ungulates is known to be largely affected by the spatial distribution of females, information on the year-round habitat selection of alternative reproductive types is scant. Here, we investigate the seasonal variation in habitat choice of a large mammal with ARTs (territoriality and nonterritoriality), the Northern chamois Rupicapra rupicapra. Global Positioning System (GPS) data on 28 adult males were collected between February 2010 and December 2013 in the Gran Paradiso National Park (Italy) and used to fit resource selection functions to explore the ART-specific use of key topographic features, such as elevation, aspect, and slope, and vegetation phenology expressed as NDVI values. Territorial and nonterritorial chamois profoundly differed in their habitat selection not only during the rutting season. Compared to nonterritorial males, territorial males used lower elevations in summer and autumn, preferred southern slopes in spring and summer, and used steeper areas in summer but not in winter. We found no difference in seasonal selection of NDVI values between males adopting ARTs. Our results suggest that territorial males tend to occupy warmer, lower-food-quality habitats in late spring and summer, whereas nonterritorial males are free to follow and exploit vegetation phenology and more favorable temperatures. Different patterns of habitat selection may reflect different trade-offs between the optimization of energy balances throughout the year and the increase of mating opportunities during the rut in males adopting alternative reproductive tactics.

Anonymous fecal sampling and NIRS studies of diet quality: Problem or opportunity?

Investigating the drivers of diet quality is a key issue in wildlife ecology and conservation. Fecal near infrared reflectance spectroscopy (f-NIRS) is widely used to assess dietary quality since it allows for noninvasive, rapid, and low-cost analysis of nutrients. Samples for f-NIRS can be collected and analyzed with or without knowledge of animal identities. While anonymous sampling allows to reduce the costs of individual identification, as it neither requires physical captures nor DNA genotyping, it neglects the potential effects of individual variation. As a consequence, regression models fitted to investigate the drivers of dietary quality may suffer severe issues of pseudoreplication. I investigated the relationship between crude protein and ecological predictors at different time periods to assess the level of individual heterogeneity in diet quality of 22 marked chamois Rupicapra rupicapra monitored over 2 years. Models with and without individual grouping effect were fitted to simulate identifiable and anonymous fecal sampling, and model estimates were compared to evaluate the consequences of anonymizing data collection and analysis. The variance explained by the individual random effect and the value of diet repeatability varied with seasons and peaked in winter. Despite the occurrence of individual variation in dietary quality, ecological parameter estimates under identifiable or anonymous sampling were consistently similar. This study suggests that anonymous fecal sampling may provide robust estimates of the relationship between dietary quality and ecological correlates. However, since the level of individual heterogeneity in dietary quality may vary with species- or study-specific features, inconsequential pseudoreplication should not be assumed in other taxa. When individual differences are known to be inconsequential, anonymous sampling allows to optimize the trade-off between sampling intensity and representativeness. When pseudoreplication is consequential, however, no conclusive remedy exists to effectively resolve nonindependence.