Abstract
Major histocompatibility complex (MHC) genes are commonly used markers for monitoring adaptive genetic and evolutionary potential of species. In this study, we investigated genetic variation ...of the MHC class II DRB locus in the chamois genus Rupicapra by using next-generation sequencing. Sequencing of 102 samples led to the identification of 25 alleles, 11 of which are novel. The high ratio of the relative rates of nonsynonymous to synonymous mutations (dN/dS) suggests a signal of positive selection on this locus. We analyzed patterns of genetic variation within and among 2 subspecies of Northern Chamois and compared them to previously published studies using neutral markers to provide a basis for assessing the effects of demographic processes. Our analyses have shown that alleles are likely to be maintained by balancing selection in different populations with similar frequencies and that this mechanism also works in small, isolated populations that are strongly affected by genetic drift.
In this study on the chamois genus Rupicapra, researchers explored genetic variation of the MHC class II DRB locus using next-generation sequencing. The research highlights a strong signal of positive selection at this locus, indicated by the high dN/dS ratio. The study also revealed that balancing selection maintains alleles across different chamois populations, including those that are small and isolated, emphasizing the evolutionary significance of this genetic mechanism.
The inferred phylogenetic relationships between organisms often depend on the molecular marker studied due to the diverse evolutionary mode and unlike evolutionary histories of different parts of the ...genome. Previous studies have shown conflicting patterns of differentiation of mtDNA and several nuclear markers in chamois (genus Rupicapra) that indicate a complex evolutionary picture. Chamois are mountain caprine that inhabit most of the medium to high altitude mountain ranges of southern Eurasia. The most accepted taxonomical classification considers two species, R. pyrenaica (with the subspecies parva, pyrenaica and ornata) from southwestern Europe and R. rupicapra (with the subspecies cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica and caucasica) from northeastern Europe. Phylogenies of mtDNA revealed three very old clades (from the early Pleistocene, 1.9 Mya) with a clear geographical signal. Here we analyze a set of 23 autosomal introns, comprising 15,411 nucleotides, in 14 individuals covering the 10 chamois subspecies. Introns offered an evolutionary scenario that contrasts with mtDNA. The nucleotidic diversity was 0.0013± 0.0002, at the low range of what is found in other mammals even if a single species is considered. A coalescent multilocus analysis with *BEAST indicated that introns diversified 88 Kya, in the late Pleistocene, and the effective population size at the root was lower than 10,000 individuals. The dispersal of some few migrant males should have rapidly spread trough the populations of chamois, given the homogeneity of intron sequences. The striking differences between mitochondrial and nuclear markers can be attributed to strong female philopatry and extensive male dispersal. Our results highlight the need of analyzing multiple and varied genome components to capture the complex evolutionary history of organisms.
The Dinaric Mountains in Slovenia, Croatia, and Bosnia and Herzegovina provide a unique system to address the effects of past hunting on the genetic structure of northern chamois (Rupicapra ...rupicapra) and possible hybridization in the contact zone in the Velebit Mountains. The northern Dinaric Mountains should be occupied by alpine chamois (Rupicapra rupicapra rupicapra), whereas the central and southern areas are inhabited by the Balkan chamois (R. rupicapra balcanica). This is the first study to characterize the genetic variation in chamois populations in the area. We used microsatellite and mitochondrial markers to analyze the genetic variation and structure of chamois populations from different geographical areas with different histories. Specifically, we explored the influence of recent human translocations and geographical isolation on the genetic architecture of chamois populations in the assumed contact zone. We successfully genotyped 74 individual samples and the number of alleles/locus ranged from 6 to 20 with a mean of 9.20. Allelic richness across populations ranged from 2.94 in the Prenj Mountains, Bosnia and Herzegovina to 3.56 in the Biokovo Mountains, Croatia. A similar pattern was also observed for heterozygosity, ranging between 0.729 and 0.572, and expected heterozygosity, ranging between 0.762 and 0.644 in the Prenj and Biokovo mountains, respectively. The global genetic distance (FST) for 7 population samples was 0.103 ±0.047 (range = 0.0156–0.185). The STRUCTURE tree clusters separated samples from the northern Dinaric Mountains from those of the southern Dinaric Mountains into 2 clusters according to geographic location. The results obtained using a Bayesian clustering methodology was similar. By using mtDNA variation in chamois from Slovenia, Croatia, and Bosnia and Herzegovina, the existence of alpine chamois haplotypes in northern areas and Balkan chamois haplotypes in southern areas was confirmed. These results confirm the impact of recent human management (i.e., translocation) into the Velebit Mountains, which established a new contact (hybridization) zone between the subspecies. Therefore, future translocations must be planned carefully to avoid compromising genetic integrity and posing a serious risk to native species, as in this case.
Recreational activities often result in a spatial and/or temporal activity shift in wildlife. With the concurrent development of outdoor activities and increase in temperatures due to climate change, ...mountain species face increasing pressures in terms of managing their activity pattern to limit both risk exposure and thermal discomfort. Using more than 15 years of long-term GPS and activity sensor data, we investigated how female northern chamois, Rupicapra rupicapra rupicapra, adjust their summer circadian activity to spatiotemporal variation in both temperatures and hikers’ presence. Chamois' behaviour was more affected by high temperatures than by hikers’ presence. During the hottest days, they shifted their activity peak earlier in the morning, were more active at night and during activity peaks, less active during daytime and had longer morning and evening peaks compared to the coldest days. Yet, total daily activity was only slightly different during the hottest days compared to the coldest days. Conversely, hikers' disturbance had weak effects on activity levels and on the timing of activity peaks. This is especially true for temporal disturbance (weekdays versus weekends and public holidays), possibly because most weekdays in summer fell during school holidays. Only during the hottest conditions, the morning activity peak was shorter and the evening peak longer in females living in the most exposed areas compared to females living in the least exposed areas. One possible explanation for the overall low effect of hikers' disturbance may be that behavioural changes buffering animals from high temperatures and hikers' presence (e.g. moving away from trails) allow them to just marginally modify their activity pattern. In the context of ongoing socioenvironmental changes, it is critical to conserve habitats providing thermal refuges against summer heat and protection from disturbance to mitigate potential detrimental consequences.
•Chamois shifted their activity peak earlier in the morning during the hottest days.•Activity increased at night and decreased during the day with high temperatures.•Chamois' crepuscular activity was higher during the hottest than the coldest days.•Spatiotemporal variation in hikers' presence had few effects on chamois' activity.•Females in the most disturbed areas shortened morning activity on the hottest days.
Animals perceive human activities as risky and generally respond with fear‐induced proactive behaviors to buffer the circadian patterns of lethal and nonlethal disturbances, such as diel migrations ...(DMs) between risky places during safe nighttime and safer places during risky daytime. However, such responses potentially incur costs through movement or reduced foraging time, so individuals should adjust their tolerance when human activities are harmless, through habituation. Yet this is a challenging cognitive task when lethal and nonlethal risks co‐occur, forming complex landscapes of fear. The consequences of this human‐induced complexity have, however, rarely been assessed. We studied the individual DM dynamics of chamois (Rupicapra rupicapra rupicapra), 89 GPS‐tracked individual‐years, from/to trails in the French Alps in areas with co‐occurring lethal (hunting) and nonlethal (hiking and skiing) disturbances, with different intensities across seasons. We developed a conceptual framework relying on the risk‐disturbance hypothesis and habituation to predict tolerance adjustments of chamois under various disturbance contexts and across contrasted seasonal periods. Based on spatial and statistical analyses combining periodograms and multinomial logistic models, we found that DM in relation to distance to a trail was a consistent response by chamois (~85% of individuals) to avoid human disturbance during daytime, especially during the hiking and hunting periods. Such behavior revealed a low tolerance of most chamois to human activities, although there was considerable interindividual heterogeneity in DM. Interestingly, there was an increased tolerance among the most disturbed diel migrants, potentially through habituation, with chamois performing shorter DMs in areas highly disturbed by hikers. Crucially, chamois that were most human‐habituated during the hiking period remained more tolerant in the subsequent harvesting period, which could increase their risk of being harvested. In contrast, individuals less tolerant to hiking performed longer DMs when hunting risk increased, and compared to hiking, hunting exacerbated the threshold distance to trails triggering DMs. No carryover effect of hunting beyond the hunting period was observed. In conclusion, complex human‐induced landscapes of fear with co‐occurring disturbances by nature‐based tourism and hunting may shape unexpected patterns of tolerance to human activities, whereby animal tolerance could become potentially deleterious for individual survival.
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•The comparison of the three mitochondrial lineages of chamois highlights its presence in Europe since the early Pleistocene.•The mtDNA phylogeny of chamois does not concur with its ...taxonomy.•The mtDNA of resident females of Chartreuse Mountains was introgressed into immigrant males.
Mitochondrial DNA (mtDNA) has largely been used for species delimitation. However, mtDNA introgression across species boundaries can lead to inconsistent phylogenies. Partial sequences of the mitochondrial genome in the chamois, genus Rupicapra, show the presence of three well differentiated clades, West (mtW), Central (mtC) and East (mtE), each with a geographically restricted distribution. The complete mtDNAs of the clades mtW and mtE (main representatives of the two currently considered species R. pyrenaica and R. rupicapra respectively) have been reported. In the present study, we sequenced the clade mtC present in populations from both species inhabiting the central area of Europe: the Apennines (R. pyrenaica ornata) and the Chartreuse Mountains (R. rupicapra cartusiana). The phylogenetic comparison with the genomes of Caprini highlights the ancient presence of chamois in Europe relative to the fossil record, and the old age of the chamois clade mtC that was split from the clade mtW in the early Pleistocene. The separation of R. pyrenaica ornata and R. rupicapra cartusiana female lineages was recent, dating of the late Pleistocene. Our data represent an example of mtDNA introgression of resident females of Chartreuse Mountains into immigrant males of R. rupicapra due to male-biased migration and female phylopatry.
The “niche variation hypothesis” (NVH) predicts that populations with wider niches should display higher among-individual variability. This prediction originally stated at the intra-specific level ...may be extended to the inter-specific level: individuals of generalist species may differ to a greater extent than individuals of a specialist species. We tested the NVH at intra- and inter-specific levels based on a large diet database of three large herbivore feces collected in the field and analyzed using DNA metabarcoding. The three herbivores (roe deer Capreolus capreolus, chamois Rupicapra rupicapra and mouflon Ovis musimon) are highly contrasted in terms of sociality (solitary to highly gregarious) and diet. The NVH at the intraspecific level was tested by relating, for the same population, diet breadth and inter-individual variation across the four seasons. Compared to null models, our data supported the NVH both at the intra- and inter-specific levels. Inter-individual variation of the diet of solitary species was not larger than in social species, although social individuals feed together and could therefore have more similar diets. Hence, the NVH better explained diet breadth than other factors such as sociality. The expansion of the population niche of the three species was driven by resource availability, and achieved by an increase in inter-individual variation, and the level of inter-individual variability was larger in the generalist species (mouflon) than in the specialist one (roe deer). This mechanism at the base of the NVH appears at play at different levels of biological organization, from populations to communities.
Understanding components of interspecific competition has long been a major goal in ecological studies. Classical models of competition typically consider equal responses of all individuals to the ...density of competitors, however responses may differ both among individuals from the same population, and between populations.
Based on individual long‐term monitoring of two chamois populations in sympatry with red deer, we built a multi‐event capture‐recapture model to assess how vital rates of the smaller chamois are affected by competition from the larger red deer.
In both populations, mortality and breeding probabilities of female chamois depend on age and in most cases, breeding status the preceding year. Successful breeders always performed better the next year, indicating that some females are of high quality. In one population where there was high spatial overlap between the two species, the survival of old female chamois that were successful breeders the preceding year (high‐quality) was negatively related to an index of red deer population size suggesting that they tend to skip reproduction instead of jeopardizing their own survival when the number of competitors increases. The breeding probability of young breeders (ages 2 and 3) was similarly affected by red deer population size. In contrast, in the second site with low spatial overlap between the two species, the vital rates of female chamois were not related to red deer population size.
We provide evidence for population‐specific responses to interspecific competition and more generally, for context‐, age‐ and state‐dependent effects of interspecific competition.
Our results also suggest that the classical assumption of equal responses of all individuals to interspecific competition should be relaxed, and emphasize the need to move towards more mechanistic approaches to better understand how natural populations respond to changes in their environment.
Thanks to long‐term monitoring of two interacting species (chamois and red deer) at several locations and multi‐event capture‐recapture modelling, the authors show that breeding probabilities of female chamois could be affected by the presence of red deer competitors. These effects of red deer abundance on chamois were population‐, age‐ and state‐dependent.
Trombiculosis has been reported in some wild ruminant species. We investigated the occurrence of trombiculosis in the northern chamois ( Rupicapra rupicapra rupicapra) in the Western Italian Alps, ...and we describe the related histopathologic changes. Superficial scrapes and skin samples were taken from 191 chamois from the Lombardy and Piedmont regions during the hunting season in September-December 2015. Numbers of eosinophils, mast cells, cluster of differentiation (CD)3-, CD79α-, CD68-positive cells were determined on immunohistochemically stained skin sections using a semiautomatic analysis system. Forty (20.9, 40/191) chamois were positive for trombiculid larvae on skin scrapings. Of the positive animals, 15 were from Lombardy and 25 from Piedmont, with similar prevalences. Macroscopic lesions were light with involvement of body regions that had contact with the ground, especially head (pinnae and areas around eyes and mouth) and limbs, where stylostome was easily formed due to thin skin. Histologically, trombiculosis caused a focal moderate dermatitis with epidermal necrosis, thin crusts, and hyperkeratosis. Inflammatory infiltrates were suggestive of a granulomatous reaction centered on a stylostome, formed by mite saliva and necrotic host tissue debris. However, we detected some difference in cutaneous immune response with some chamois showing a prevalent T-cell response and others having an increased B-cell count associated with a higher number of eosinophils, mast cells and a lower number of T cells.
As an inhabitant of the Alps, chamois are exposed to significant climatic changes throughout the year and are also strongly confronted with changing forage availability. Besides horizontal and ...vertical migratory movements as an adaptation, it undergoes physiological transformations and dynamic changes in the ruminal microbiota.
The following study used 48 chamois of different ages and genders to investigate to which extent the ingested food plants, the resulting crude nutrients in the rumen (reticulorumen) contents, and the bacterial microbiota in the rumen and their fermentation products were influenced by the changes over the seasons. Very little is known about the microbiota of wild ruminants, and many bacterial taxa could only be determined to certain taxonomic levels in this study. However, adapted microbiota reflects the significant changes in the ingested forage and the resulting crude nutrients. For some taxa, our results indicated potential functional relationships. In addition, 15 genera were identified, representing almost 90% of the relative abundance, forming the central part of the microbial community throughout the year. The successful and flexible adaptation of chamois is reflected in the chamois rumen’s nutrient and microbial profile. This is also the first study that analyzes the microbiota of the chamois using rumen samples and considers the microbiota in a seasonal comparison.
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