Recombination and the origin of sequence diversity in the DRB MHC class II locus in chamois (Rupicapra spp.)

We examined the evolutionary processes contributing to genetic diversity at the major histocompatibility complex (MHC) class II DRB locus in chamois (Rupicapra spp., subfamily Caprinae). We characterised the pattern of intragenic recombination (or homologous gene conversion) and quantified the amount of recombination in the genealogical history of the two chamois species, Pyrenean chamois (Rupicapra pyrenaica) and Alpine chamois (Rupicapra rupicapra). We found evidence for intragenic recombination, and the estimated amount of population recombination suggests that recombination has been a significant process in generating DRB allelic diversity in the genealogical history of the genus Rupicapra. Moreover, positive selection appears to act on the same peptide-binding residues in both analysed chamois species, but not in identical intensity. Recombination coupled with positive selection drives the rapid evolution at the peptide-binding sites in the MHC class II DRB gene. Many chamois MHC class II DRB alleles are thus much younger than previously assumed.     

Predicting seasonal and spatial variations in diet quality of Pyrenean chamois (Rupicapra pyrenaica pyrenaica) using near infrared reflectance spectroscopy

Monitoring nutritional status of wildlife is key to understanding the population response to changes in food availability. Several direct and indirect methods have been proposed for such purposes, but faecal nitrogen (FN) is by far the most commonly used indirect non-invasive indicator of free-ranging ruminant diet quality. In this work, two methods were used to estimate the FN content in 291 pellet samples of Pyrenean chamois (Rupicapra pyrenaica pyrenaica) collected during a 2-year period (May 2009 to May 2011) in two chamois populations from the Catalan Pyrenees, Spain: the Dumas LECO analyzer and near-infrared reflectance spectroscopy (NIRS). In order to optimize further FN estimations we performed three different NIRS calibrations: (1) general, across year, season and populations; (2) population-specific; and (3) season-specific, i.e., different periods of vegetation growth. FN ranged from 1.66 % to 2.85 % (dry matter basis) and was higher in the main vegetation growing season than in winter. Concerning NIRS calibration, our study confirmed that FN of Pyrenean chamois can be accurately determined by NIRS, since the general calibration was accurate enough to predict FN. It is concluded that NIRS represents a non-destructive, emission-free and low-cost analytical technique which may reduce the use of conventional laborious methods for estimating FN in long-term wildlife monitoring.     

Dynamics of an Infectious Keratoconjunctivitis Outbreak by Mycoplasma conjunctivae on Pyrenean Chamois Rupicapra p. pyrenaica

Between 2006 and 2008, an outbreak of Infectious Keratoconjunctivitis (IKC) affected Pyrenean chamois Rupicapra p. pyrenaica, an endemic subspecies of mountain ungulate that lives in the Pyrenees. The study focused on 14 mountain massifs (180,000 ha) where the species’ population is stable. Cases of IKC were detected in ten of the massifs and, in five of them, mortality was substantial. The outbreak spread quickly from the first location detected, with two peaks in mortality that affected one (2007) and three (2008) massifs. In the latter, the peak was seasonal (spring to autumn) and, in the former, the outbreak persisted through winter. To identify the outbreak’s aetiology, we examined 105 Pyrenean chamois clinically affected with IKC. TaqMan rt-PCR identified Mycoplasma conjunctivae in 93 (88.5%) of the chamois. Another rt-PCR detected Chlamydophila spp. in 14 of chamois, and 12 of those had mixed infections with mycoplasmas. In the period 2000–2007, the chamois population increased slightly (λ 1.026) but decreased significantly during the IKC outbreak (λ 0.8, 2007–2008; λ 0.85, 2008–2009) before increasing significantly after the outbreak (λ 1.1, 2009–2010). Sex-biased mortality shifted the adult sex ratio toward males (from 0.6 to 0.7 males per female) and reduced productivity slightly. Hunting was practically banned in the massifs where chamois experienced significant mortality and allowed again after the outbreak ended. Long-term monitoring of wild populations provides a basis for understanding the impacts of disease outbreaks and improves management decisions, particularly when species are subject to extractive exploitation.     

Two Different Epidemiological Scenarios of Border Disease in the Populations of Pyrenean chamois (Rupicapra p. pyrenaica) after the First Disease Outbreaks

Since 2001 several outbreaks of a new disease associated with Border disease virus (BDV) infection have caused important declines in Pyrenean chamois (Rupicapra pyrenaica) populations in the Pyrenees. The goal of this study was to analyze the post-outbreak BDV epidemiology in the first two areas affected by disease with the aim to establish if the infection has become endemic. We also investigated if BDV infected wild and domestic ruminants sharing habitat with chamois. Unexpectedly, we found different epidemiological scenarios in each population. Since the disease outbreaks, some chamois populations recuperated quickly, while others did not recover as expected. In chamois from the first areas, prevalence was high (73.47%) and constant throughout the whole study period and did not differ between chamois born before and after the BDV outbreak; in all, BDV was detected by RT-PCR in six chamois. In the other areas, prevalence was lower (52.79%) and decreased during the study period; as well, prevalence was significantly lower in chamois born after the disease outbreak. No BDV were detected in this population. A comparative virus neutralisation test performed with four BDV strains and one Bovine viral diarrhoea virus (BVDV) strain showed that all the chamois had BDV-specific antibodies. Pestivirus antibodies were detected in all the rest of analyzed species, with low prevalence values in wild ruminants and moderate values in domestic ruminants. No viruses were detected in these species. These results confirm the hypothesis that outbreaks of BDV infection only affect the Pyrenean chamois, although other wild ruminants can occasionally be infected. In conclusion, two different scenarios have appeared since the first border disease outbreaks in Pyrenean chamois: on the one hand frequent BDV circulation with possible negative impact on population dynamics in some areas and on the other, lack of virus circulation and quick recovery of the chamois population.     

Temporal pooling of point transect data increases precision in density estimates of southern chamois

Estimating animal abundances in small areas is a difficult task and because a limited number of observations often results in low-precision estimates whose inaccuracies may even be exacerbated if surveys are focussed on clustered populations and/or are only carried out once a year. In an attempt to overcome this problem, we used point transects to monthly survey two small areas of a game reserve to assess the density of Pyrenean chamois (Rupicapra p. pyrenaica). The coefficient of variation associated with the density estimates after pooling observations by season was still high but decreased to reasonable values (<20%) when observations were over 29 chamois groups (clusters). Our results suggest that Distance Sampling may be a useful way of estimating the population density of mountain ungulates such as Pyrenean chamois in small rugged areas where only a small or moderate number of observations are to be expected.     

Molecular identification of a new pestivirus associated with increased mortality in the Pyrenean Chamois (Rupicapra pyrenaica pyrenaica) in Spain

Pestivirus infection was identified in 16 of 17 chamois during an outbreak of a previously unreported disease in Pyrenean chamois (Rupicapra pyrenaica pyrenaica) in northeastern Spain in 2001-02. By analysis of the 5' noncoding regions of the virus, we assigned it to the border disease virus cluster with pairwise similarity values ranging from 82.1% to 88.1%. It will be important to investigate the association of this pestivirus with disease in Pyrenean chamois.     

Increased hormonal stress response of Apennine chamois induced by interspecific interactions and anthropogenic disturbance

Responses of animals to environmental changes and their interactions with other species play an important role in conservation. Sharing a common habitat may lead to interspecific competition for resources, but field assessment of these biological events is not always easily accomplished. By using a non-invasive method, we evaluated the physiological stress responses of Apennine chamois (Rupicapra pyrenaica ornata) to the presence of cattle, sheep and goat, red deer (Cervus elaphus), people (hikers), and predators to identify which factors may affect this endangered species. During September 2012, November 2012, and July 2013, a total of 318 faecal samples were collected in representative sites and analysed for faecal cortisol metabolites (FCM). FCM concentration was analysed through linear mixed-effect models. A significant increase in FCM values in Apennine chamois sharing their habitat with domestic animals was recorded during all study periods. On the contrary, stress responses to red deer and people were limited in time and emerged only during summer months, when hikers are more frequent and red deer extend their altitudinal range reaching chamois’ habitat. The observed effects of domestic animals, red deer, and hikers should be considered in future Apennine chamois management plans, which should include the regulation of pastured domestic livestock, anthropogenic disturbances, and possible interferences with other wild species within parks.     

Nitrogen content in feces and the diet of Sika deer on the Boso Peninsula, central Japan

Fecal and rumen nitrogen content of Sika deer (Cervus nippon Temminck 1838) on the Boso Peninsula, central Japan, were analyzed concerning their seasonal fluctuations and local differences at four areas on the Boso Peninsula. The mean fecal nitrogen was high in August and low in February in all the areas. The seasonal variation, however, was relatively small. This may be the result of the following reasons: the Boso deer feed on evergreen broad-leaves containing a high and stable nitrogen content in winter; little snow falls there; and the deer consume foods relatively low in nitrogen in summer. The fecal and rumen nitrogen content in both summer and winter depended on deer density.     

Mycoplasma conjunctivae infection is not maintained in alpine chamois in eastern Switzerland

The occurrence of infectious keratoconjunctivitis (IKC) was assessed in alpine chamois (Rupicapra rupicapra rupicapra) in Grisons (Switzerland) from 1950 to 1999. The first IKC outbreaks were reported in the 1950's. Since then, the number of affected subpopulations constantly increased and, by 1999, IKC outbreaks were reported in 39 of 51 (77%) chamois sub-populations. From 1992-99, a total of 243 chamois which died of the consequences of IKC were recorded. The number of cases differed between years, and a distinct seasonal trend was observed. Infectious keratoconjunctivitis was more common during summer and autumn, with 48% of the cases recorded in August-October. Juveniles (< 4 yr of age) were mostly represented. To verify the presence of Mycoplasma conjunctivae in chamois we analyzed conjunctival swabs taken from animals affected with IKC. Among a sample of 28 affected chamois, M. conjunctivae was identified 14 times (50%). An indirect enzyme-linked immunosorbent assay (ELISA) was developed to detect specific M. conjunctivae antibodies in sera of alpine chamois with IKC. We performed a serologic investigation to assess whether M. conjunctivae infection is self-maintained in the chamois population in Grisons. In subpopulations with IKC oubreaks, seroprevalence was low (8%). Seroprevalence was even lower in subpopulations with recent IKC outbreaks (3%). We concluded that the M. conjunctivae infection is not self-maintained in alpine chamois in Grisons. The agent may originate in domestic sheep living in proximity to chamois during summer. Control of IKC in chamois should consider immunoprophylaxis in sheep or limiting interspecific transmission of M. conjunctivae.     

Pasture Quality Affects Juvenile Survival through Reduced Maternal Care in a Mountain‐Dwelling Ungulate

Lactation exerts heavy energetic and physiological costs to mothers, whilst determining early growth and survival of offspring. To mountain ungulates, access to high‐quality forage during nursing and weaning is crucial for reproductive success. We have evaluated the effects of pasture quality on suckling behaviour and winter survival of Apennine chamois Rupicapra pyrenaica ornata kids, across three areas. Areas A‐B (‘poor’ areas) were characterised by a reduced availability of nutritious forage, thus a lower diet quality for female chamois and kids; Area C (a ‘rich’ area) included a much greater availability of nutritious forage. In poor areas, pasture quality has been reduced by climatic and plant composition changes, as well as the presence of a herbivore competitor (red deer Cervus elaphus). In poor areas, we recorded a significantly (1) lower suckling success of chamois kids (number of suckling bouts/number of suck attempts); (2) lower frequency of suckling bouts (n. suckling bouts/kid/h); and (3) lower suckling intensity (suck duration/kid/h) in respect to the rich area. Conversely, frequencies of suckling rejections and those of suckling attempts (n. events/kid/h) were the lowest in the rich area. Winter survival of chamois kids was c. 2 times greater in the rich area (45%) than in poor areas (20–26%). In the poor areas, resource scarcity induced adult female chamois to decrease maternal cares and favour their own maintenance, ultimately affecting population dynamics through kid winter mortality.     

Mineral Levels in Pyrenean Chamois (Rupicapra pyrenaica)

The effects of mineral deficiencies are often sub-clinical, and the importance of mineral status is often underestimated in wildlife populations. To our knowledge, this is the first study that gives reference intervals of hepatic minerals for Pyrenean chamois (Rupicapra pyrenaica). We determined macro and trace mineral concentrations in liver samples from 100 animals (44 healthy and 56 sick) collected in the Catalan Pyrenees (NE Spain) from 1995 to 2008. After wet digestion, we determined Na, K, Ca, P, Mg, S, and Fe concentrations by inductively coupled plasma optical emission spectrometry (ICP-OES) and Cu, Zn, and Mo concentrations by inductively coupled plasma mass spectrometry (ICP-MS). We observed low hepatic concentrations of Cu in a considerable percentage of chamois, without evidences that these low concentrations increased their susceptibility to infectious diseases. The group of sick chamois had very similar percentage of animals (10/56) with low concentration of Cu (<20 ppm DW) than the group of healthy chamois (9/44). On the other hand, we observed that infectious diseases increased significantly the hepatic concentrations of Na, Ca, Mg, Fe and Zn, very likely, as a consequence of processes associated with the acute phase inflammatory response. The obtained values of liver mineral levels and their sources of variation, such as sex, age and disease, mostly fall within the range of those described for other ruminants, but possible deficiencies and differences between individuals and populations require further study.     

Reflections of ecological differences? Stress responses of sympatric Alpine chamois and red deer to weather,forage quality,and human disturbance

Depending on the habitats they live in, temperate ungulates have adapted to different degrees to seasonally changing forage and weather conditions, and to specific escape strategies from predators. Alpine chamois, a mountain ungulate, and red deer, originally adapted to open plains, would therefore be expected to differ in their physiological responses to potential stressors. Based on 742 chamois and 1557 red deer fecal samples collected year‐round every 2 weeks for 4 years at the same locations within a strictly protected area in the Swiss Alps, we analyzed glucocorticoid metabolite (FGM) concentrations for both species. Results from linear mixed effects models revealed no physiological stress response to changing visitor numbers, but instead to drought conditions for both species during summer. In winter, FGM concentrations increased with increasing snow height in both species, but this response was modulated by temperature in red deer. Chamois showed a stronger stress response to increasing snow height during November and December than between January and March, while FGM concentrations increased with decreasing temperature throughout winter. An increase in FGM concentrations with decreasing forage digestibility during winter was found only for red deer. The results are thus partly in contradiction to expectations based on feeding type and adaptations to different habitats between the two species. The lack of a response to forage digestibility in chamois may reflect either better adaptation to difficult feeding conditions in subalpine forests, or, by contrast, strong constraints imposed by forage quality. The similar responses of both species to weather conditions in winter suggest that climatic factors at the elevations examined here are sufficiently harsh to be limiting to temperate ungulates regardless of their specific adaptations to this environment.     

Concentration of fecal cortisol metabolites in chamois in relation to tourist pressure in Tatra National Park (South Poland)

In protected areas, outdoor recreation, and nature-based tourism can act as potential stressors for wildlife. Given the growing demand for nature recreation, the consequences of high tourist visitation on wildlife need to be assessed in order to avoid incompatibilities between public use and species protection goals. The Tatra National Park (Poland), in the Carpathian Mountains, is a unique alpine ecosystem visited by three million tourists per year. It hosts the only native population of an endemic subspecies of chamois (Rupicapra rupicapra tatrica). We investigated the effects of tourist disturbance, the number of visitors, and the season on the concentration of fecal cortisol metabolites (FCM) in Tatra chamois in 2009. FCM levels of chamois were significantly higher and showed higher variation at high tourist disturbance (mean?±?SD, 46.2?±?31.53 ng/g, n?=?56) than at low disturbance sites (mean?±?SD, 17.2?±?8.05 ng/g, n?=?38). Stress levels increased with the number of visitors and therefore showed a peak in summer, coinciding with the highest number of visitation to the national park. A large portion of chamois habitat in Tatra National Park is within the area of influence of the touristic trail network. The temporal or permanent creation of areas free of disturbance in protected areas should be considered, especially in the periods of high tourist visitation. This study highlights the need to monitor the effects of tourist activities on wildlife and to implement new policies in the management of protected areas.     

A negative association between horn length and survival in a weakly dimorphic ungulate

While all models of sexual selection assume that the development and expression of enlarged secondary sexual traits are costly, males with larger ornaments or weapons generally show greater survival or longevity. These studies have mostly been performed in species with high sexual size dimorphism, subject to intense sexual selection. Here, we examined the relationships between horn growth and several survival metrics in the weakly dimorphic Pyrenean chamois (Rupicapra pyrenaica). In this unhunted population living at high density, males and females were able to grow long horns without any apparent costs in terms of longevity. However, we found a negative relationship between horn growth and survival during prime age in males. This association reduces the potential evolutionary consequences of trophy hunting in male chamois. We also found that females with long horns tended to have lower survival at old ages. Our results illustrate the contrasting conclusions that may be drawn when different survival metrics are used in analyses. The ability to detect trade‐off between the expression of male secondary sexual traits and survival may depend more on environmental conditions experienced by the population than on the strength of sexual selection.     

Preliminary results on snow surveys of Pyrenean grey partridge (<Emphasis Type="Italic">Perdix perdix hispaniensis</Emphasis>) in the Cantabrian Mountains

Peripheral populations tend to be smaller and more prone to extinction than those in core areas. Grey partridge Perdix perdix in its southern-most edge occupies mountain habitats, which is unlike any habitat in its northern European range. This makes these mountain ecotypes especially susceptible to range contractions and population decrease is likely the result of the current global change process. In Iberia, the so-called Pyrenean grey partridge subspecies P. p. hispaniensis is considered to be declining but little is known about its real trends and numbers. We locally studied the abundance of the Pyrenean grey partridges in winter by direct observations in the Cantabrian Mountains (NW Spain), while driving on a paved road. In addition, we related observed partridge abundances to different context variables to find the ones better helping to detect this species. The paved road-based censuses were successful, and we detected the presence and abundance of the Pyrenean grey partridge. Individuals and groups were more easily detected from December to February while couples were observed at the end of the winter (i.e. February–March). Wherever open paved roads exist, we strongly recommend using direct observations from them during winter as an adequate tool for Pyrenean grey partridge monitoring. This easy and cost-effective method affordable to managers and conservationists can contribute to a better understanding of the European mountain’s changing ecosystems and help us understanding the population trends of this vulnerable subspecies.     

Different effects of alpine woody plant expansion on domestic and wild ungulates

Changes in land‐use and climate affect the distribution and diversity of plant and animal species at different spatiotemporal scales. The extent to which species‐specific phenotypic plasticity and biotic interactions mediate organismal adaptation to changing environments, however, remains poorly understood. Woody plant expansion is threatening the extent of alpine grasslands worldwide, and evaluating and predicting its effects on herbivores is of crucial importance. Here, we explore the impact of shrubification on the feeding efficiency of Pyrenean chamois (Rupicapra p. pyrenaica), as well as on the three most abundant coexisting domestic ungulate species: cattle, sheep and horses. We use observational diet composition from May to October and model different scenarios of vegetation availability where shrubland and woodland proliferate at the expense of grassland. We then predicted if the four ungulate species could efficiently utilize their food landscapes with their current dietary specificities measuring their niche breath in each scenario. We observed that the wild counterpart, due to a higher trophic plasticity, is less disturbed by shrubification compared to livestock, which rely primarily on herbaceous plants and will be affected 3.6 times more. Our results suggest that mixed feeders, such as chamois, could benefit from fallow landscapes, and that mountain farmers are at a growing economic risk worldwide due to changing land‐use practices and climate conditions.     

Diversity and evolution of the Mhc-DRB1 gene in the two endemic Iberian subspecies of Pyrenean chamois, Rupicapra pyrenaica

Major histocompatibility complex class II locus DRB variation was investigated by single-strand conformation polymorphism analysis and sequence analysis in the two subspecies of Pyrenean chamois (Rupicapra pyrenaica) endemic to the Iberian Peninsula. Low levels of genetic variation were detected in both subspecies, with seven different alleles in R. p. pyrenaica and only three in the R. p. parva. After applying the rarefaction method to cope with the differences in sample size, the low allele number of parva was highlighted. The low allelic repertoire of the R. p. parva subspecies is most likely the result of bottlenecks caused by hunting pressure and recent parasitic infections by sarcoptic mange. A phylogenetic analysis of both Pyrenean chamois and DRB alleles from 10 different caprinid species revealed that the chamois alleles form two monophyletic groups. In comparison with other Caprinae DRB sequences, the Rupicapra alleles displayed a species-specific clustering that reflects a large temporal divergence of the chamois from other caprinids, as well as a possible difference in the selective environment for these species.     

Condition of mule deer during winter: stress and spatial overlap with North American elk

We assessed body condition, diet quality (indexed by fecal nitrogen), and stress levels (using fecal glucocorticoid metabolites) in mule deer Odocoileus hemionus in southeastern Idaho, USA, during a mild (2007) and a harsh winter (2008) to evaluate spatial overlap and potential competition with North American elk Cervus elaphus. We used data from GPS telemetry to construct spatially explicit maps of local population density of elk for January–April. Loss of body condition over winter in yearling and adult female mule deer was not related to elk density but to winter severity. Fecal nitrogen increased as winter progressed in both winters, was significantly lower during 2008 than in 2007, but was not related to local population density of elk. In the mild winter of 2007, a significant positive relationship existed between local population density of elk and fecal glucocorticoid metabolite levels of mule deer, indicating increased physiological stress among mule deer wintering in close proximity to elk. Fecal glucocorticoid metabolite levels in deer were lower in 2008 than in 2007 and exhibited no significant relationship with elk density. Declining fecal glucocorticoid levels through winter may be typical of northern cervids. No difference existed in levels of fecal glucocorticoids between sexes of deer. A reduction in elk populations may not improve diet quality, physiological stress levels, or body condition of mule deer on winter range, especially during severe winters. Consequently, management and conservation of winter habitat are more likely to benefit mule deer than would altering density of elk.     

Influence of Exogenous Triiodothyronine (T<Subscript>3</Subscript>) on Fecal Shedding of <Emphasis Type="Italic">Escherichia coli</Emphasis> O157 in Cattle

Fecal prevalence of Escherichia coli O157 in ruminants is highest in the summer months and decreases to low or undetectable levels in the winter. We hypothesize that the seasonal variation of this pathogen is a result of physiological responses within the host animal to changing day length. The thyroid is an endocrine gland known to respond to changing day length. Two experiments were conducted to determine if a hyperthyroid status would initiate fecal shedding of E. coli O157 in cattle during the winter when shedding is virtually nonexistent (winter experiment) or influence cattle actively shedding E. coli O157 (summer experiment). Yearling cattle were group-penned under dry-lot conditions, adjusted to a high concentrate ration, and randomly assigned to treatment: control (1 mL corn oil injected s.c. daily) or triiodothyronine (T₃; 1.5 mg suspended in corn oil injected s.c daily). Cattle were individually processed daily for collection of fecal and blood samples. Treatment with exogenous T₃ produced a significant change in serum thyroid hormone concentrations indicative of a hyperthyroid status in both experiments. No differences (P>0.10) were observed in fecal shedding of E. coli O157 in the winter experiment. In the summer experiment, fecal shedding of E. coli O157 was decreased (P=0.05) by administration of T₃ during the treatment period (days 1–10), tended to be lower (P=0.08) during the following 7-day period of no treatment, and was lower (P=0.01) when examined across the entire experimental period. Results of this research indicate that the thyroid or its hormones may be involved in the seasonal shedding patterns of E. coli O157 in cattle.     

Social Interactions in Isard Kids Rupicapra pyrenaica pyrenaica (Artiodactyla: Bovidae): Possible Influence on Development of Social Bonding

Assuming that social experiences at an early age may be a determinant factor in the process of formation of social network and attachments, we studied the social interactions of isard, or Pyrenean chamois, kids (Rupicapra pyrenaica pyrenaica) during their first year, to understand “how” sociality arises in isards rather than “why”. Interactions with the mother were affiliative, and approaches of kid to mother or vice versa were generally followed by another “positive” interaction. Interactions between kids were also frequent and playful. Interactions with both mother and peers provided positive reinforcement which may strengthen bonds. However, early interactions of kids with yearlings and other adults provided negative experience, no attachment thus developing from them. Social affinities of adults as well as the social and spatial organization of groups may be understood when ontogenetical history and immediate causality are highlighted.