Late Pleistocene and Holocene chamois in Italy

相似文献   

Integrating phylogeographic patterns of microsatellite and mtDNA divergence to infer the evolutionary history of chamois (genus <Emphasis Type="Italic">Rupicapra</Emphasis>)

Background  

The chamois, distributed over most of the medium to high altitude mountain ranges of southern Eurasia, provides an excellent model for exploring the effects of historical and evolutionary events on diversification. Populations have been grouped into two species, Rupicapra pyrenaica from southwestern Europe and R. rupicapra from eastern Europe. However, a previous study of cytochrome b revealed that the two proposed species were non-monophyletic. The reconstruction of phylogenetic relationships between animal species often depends on the markers studied. To further elucidate the evolutionary history of chamois, we extended earlier studies by analysing DNA sequences of four mitochondrial regions (ND1, 12S, tRNApro and Control Region) and microsatellites (20 loci) to include all subspecies and cover its entire distribution range.     

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.     

Cytochrome b phylogeography of chamois (Rupicapra spp.). Population contractions, expansions and hybridizations governed the diversification of the genus

The chamois provides an excellent model for exploring the effect of historical and evolutionary events on diversification. We investigate cytochrome b (cytb) sequences in the 10 recognized subspecies of Rupicapra classified within 2 species: Rupicapra pyrenaica, with the subspecies parva, pyrenaica, and ornata, and Rupicapra rupicapra, with cartusiana, rupicapra, tatrica, carpatica, balcanica, asiatica, and caucasica. A fragment of 349 bp of the cytb was sequenced in 189 individuals. We identified 3 cytb lineages: Clade West in Iberia and Western Alps; Clade Central in the Apennines and the Massif of Chartreuse; and Clade East present in populations to the east of the Alps. The 2 proposed species were polyphyletic; the clades West and Central are represented in both, whereas the Clade East is restricted to R. rupicapra. In contrast to the current systematic, cytb phylogenies suggest the classification of the 10 subspecies of chamois into a single species, R. rupicapra. Phylogeny and geographical distribution of the 3 lineages show the effects of limited latitudinal range expansions, contractions, and hybridizations among highly divergent lineages, along with a major role of the glacial ice sheets of the Alps and the Pyrenees as barriers to gene flow, on the diversification of extant taxa.     

Do ecologically close species shift their daily activities when in sympatry? A test on chamois in the presence of mouflon

Temporal partitioning of daily activities between species may promote coexistence within animal communities by reducing behavioural interference, particularly when species highly overlap in the use of space and resources. Such a strategy may be used by Alpine chamois (Rupicapra rupicapra rupicapra) when in the presence of mouflon (Ovis gmelini musimon × Ovis sp.), an introduced highly gregarious species with a broader ecological niche, overlapping with that of chamois. Using simultaneous monitoring of 29 Global Positioning System‐collared chamois and 12 mouflon, we assessed the temporal variation in activity patterns of chamois amongst two subpopulations: one without mouflon and one with mouflon, during January and August, which are the two most extreme periods of spatial overlap of mouflon with chamois distribution. Substantial differences in activity patterns between chamois and mouflon were observed (mean 13.8 ± 10.5% in January and 10.6 ± 11.6% in August). More subtle differences appeared between both subpopulations of chamois and persisted, regardless of the spatial overlap with mouflon (3.2 ± 1.8% in January and 2.6 ± 1.5% in August), thus highlighting that there is no behavioural interference from mouflon on chamois. Our findings suggest that the temporal partitioning of daily activities between chamois and mouflon, although probably a result of species‐specific adaptations to environmental conditions, may contribute to their coexistence. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 621–626.     

Dung avoidance as a possible mechanism in competition between wild and domestic ungulates: two experiments with chamois <Emphasis Type="Italic">Rupicapra rupicapra</Emphasis>

Wild ungulates often adjust spatial behaviour where they coexist with livestock. In European mountains, chamois Rupicapra rupicapra or R. pyrenaica commonly avoid alpine pastures used by domestic sheep. Mechanisms leading to competitive losing out of the wild species are not well understood, but mostly, resource competition is inferred and sometimes demonstrated. We hypothesised that chamois need to minimise the risk of intestinal parasite uptake and therefore would avoid pastures contaminated with sheep dung. We tested this in two experiments by contaminating feeding patches of wild and captive chamois with (parasite-free) sheep faeces. Wild chamois did not avoid grazing sites or plots on which sheep dung had been placed at a (low) density representing the commonly encountered situation in the Swiss Alps. Captive chamois strongly reduced browsing time on small trees given for food when the surroundings of the trees were sprayed with a watery faecal solution. We concluded that the odour signalled a potential high risk of parasite infection to the captive chamois, whereas the density of sheep dung on the grazing site of wild chamois was not high enough to be perceived as a risk. The need to minimise endoparasite uptake from faeces may therefore play a role in driving spatial behaviour of wild ungulates and could result in competitive imbalance between wild and domestic ungulates.     

The Balkan chamois,an archipelago or a peninsula? Insights from nuclear and mitochondrial DNA

The Balkan chamois (Rupicapra rupicapra balcanica) is widespread on the Balkan Peninsula, along mountain massifs from Croatia in the north to Greece in the south and Bulgaria in the east. Knowledge on the genetic structure of Balkan chamois populations is limited and restricted to local studies. Therefore, the main objective of this study was to use nuclear (16 microsatellites) and mitochondrial (partial 376 base pairs control region) markers to investigate the genetic structure of this chamois subspecies throughout its distribution range and to obtain information on the degree of connectivity of the different (sub)populations. We extracted DNA from bone, dried skin and muscle tissue and successfully genotyped 92 individuals of Balkan chamois and sequenced the partial control region in 44 individuals. The Bayesian analysis suggested 3 genetic clusters and assigned individuals from Serbia and Bulgaria to two separate clusters, while individuals from the other countries belonged to the same cluster. Thirty new haplotypes were obtained from partial mitochondrial DNA sequences, with private haplotypes in all analyzed populations and only two haplotypes shared among populations, indicating the possibility of past translocations. The subspecies genetic composition presented here provides the necessary starting point to assess the conservation status of the Balkan chamois and allows the development of conservation strategies necessary for its sustainable management and conservation.

     

Phylogeography of chamois (Rupicapra spp.) inferred from microsatellites

Evolutionary relationships among populations of chamois (Rupicapra spp.) across their current range from the Caucasus to the Cantabrian Mountains were investigated. The allelic variation in 23 microsatellite loci was assessed in eight geographical populations, recognised as subspecies of the two closely related species R. pyrenaica and R. rupicapra. Analysis of variance in allele frequencies (Fst, statistics) and in repeat numbers (Rst, statistics) showed these data to be highly structured. Two genetic distances between pairs of populations, Ds and (δμ)², were computed and phylogenetic trees were constructed. Similar patterns were produced by the different statistics. All trees indicate a deep divergence between the two recognised species, which is compatible with archaeological data that place their split in the Riss–Würm interglacial period. Genetic distances between pairs of populations are highly correlated with geographical distance. This suggests that the history of the genus during Pleistocene glacial-interglacial periods was dominated by expansions and contractions within limited geographic regions, leading to alternate contact and isolation of contiguous populations. In addition, the alpine barrier has played a substantial role in West–East differentiation.     

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.     

Population genetics of chamois in the contact zone between the Alps and the Dinaric Mountains: uncovering the role of habitat fragmentation and past management

The chamois is a habitat specialist ungulate occupying “continental archipelagos” of fragmented rocky habitats which are frequently restricted to high altitudes. It is not clear whether forest habitats separating such population fragments act as barriers to gene flow. We studied the genetic makeup of the chamois in a topographically diverse landscape at the contact zone of two mountain ranges in Slovenia. Based on sequences of mitochondrial DNA, all Slovenian populations belong to a Northern chamois (Rupicapra r. rupicapra) subspecies. The range of chamois in Slovenia encompasses three different regions, each with unique topography, habitat connectivity and abundance of chamois: the Alps, the Dinaric Mts., and the Pohorje Mts. The habitat of the chamois is extensive and more or less continuous in the Alps, but suboptimal and fragmented in the remaining regions. In agreement with neutral genetic theory, large Northern chamois populations tended to have higher allelic richness and observed heterozygosity. Spatial clustering bears the differentiation into four geographically associated clusters within Slovenia and also revealed a strong substructure within all mountain ranges with suboptimal chamois habitat. Surprisingly, some small Dinaric populations have stayed genetically isolated in restricted habitat patches, even if they are geographically very close to each other. The four clusters, each having a unique demographic history, should be regarded as independent units for management purposes.     

Protostrongylus (Protostrongylus) rufescens boevi, a new subspecies, parasite of the respiratory apparatus of chamois]

A nematode parasitic of bronchial system of Rupicapra rupicapra (chamois) of Parco Nazionale del Gran Paradiso (Italian Western Alps) is described and the name Protostrongylus (Protostrongylus) rufescens boevi subspecies nova, is proposed.     

Comparative evaluation of effort, capture and handling effects of drive nets to capture roe deer (Capreolus capreolus), Southern chamois (Rupicapra pyrenaica) and Spanish ibex (Capra pyrenaica)

The objective of this study is to assess the usefulness of drive nets to capture roe deer (Capreolus capreolus), Southern chamois (Rupicapra pyrenaica) and Spanish ibex (Capra pyrenaica), comparing the results obtained with other capture methods and amongst the three species. Sixty-five drive net capture operations using beaters were conducted from January 1998 to September 2004. A total of 161 wild ungulates (31 roe deer, 95 Southern chamois and 35 Spanish ibexes) were captured. The average number of animals captured per operation was 1.07 for roe deer, 3.96 for Southern chamois and 2.92 for Spanish ibex. The average number of person–days per captured animal was 21.5, 7.1 and 10.6 for roe deer, Southern chamois and Spanish ibex, respectively. Specificity was 100% for Southern chamois and Spanish ibex (only the target species captured) and 77.5% for roe deer. Risk for the animals (mortality plus injuries) was 3.23% for roe deer, 5.27% for Southern chamois and 0% for Spanish ibex, whereas injuries to the operators occurred with 3.1% of the handled animals. Sex ratio was skewed towards females in roe deer, towards males in Southern chamois and balanced in Southern chamois. Drive nets showed good performance, although many operators were required. Safety for the animals and specificity were higher than traditionally attributed to this capture method. It is concluded that drive nets are an efficient and safe method to capture many ungulate species.     

Male Alpine Chamois Occupy Territories at Hotspots Before the Mating Season

Ungulate mating systems vary broadly both between and within species. Studies on mating systems in different habitats can provide clues to the ecological factors determining this diversity. Despite its abundance in the European Alps and its importance as a game species, surprisingly little is known about the mating system of Alpine chamois Rupicapra rupicapra rupicapra. We tested the hypothesis that adult males first defend mating territories in late spring, when females segregate from males and well before the Nov. rut. In the Gran Paradiso National Park (north‐western Italian Alps), adult males shared a winter range but occupied individual ranges in summer and early autumn. Males were more aggressive to each other in the summer than in the spring. A strong site fidelity from one year to the next was found for the summer and early autumn months. Those males that occupied the same territories both in the summer and during the rut (Nov.) appeared to be at hotspots, attractive to females during the rut because of reduced snow cover. Other males appeared to cluster around these hotspots during the rut. Territories that were first occupied during the summer were visited by more females than those that were not established until the rut began. Our results suggest that the mating system of this population of Alpine chamois consists of the early occupation of clustered mating territories. The early establishment of mating territories in areas frequented by females during the rut may lead to reproductive benefits for male chamois.     

A set of 21 polymorphic microsatellites in Alpine chamois (Rupicapra rupicapra)

A cross‐species amplification test of 39 bovid microsatellite markers was carried out on chamois (Rupicapra rupicapra), a species with a high economic and tourist value, for which a number of life‐history traits remain to be quantified. Of 39 primer pairs tested, 26 gave a specific amplification product and 21 were polymorphic. Locus‐specific allelic richness ranged from two to six. Our results suggest that these loci will be useful for investigating basic population genetics as well as life‐history traits, such as dispersal.     

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.     

Feeding habits,forage selection,and diet overlap in Alpine chamois (<Emphasis Type="Italic">Rupicapra rupicapra</Emphasis> L.) and domestic sheep

Fecal microhistological analyses have been used to assess the summer diet of chamois (Rupicapra rupicapra L., 1758) and domestic sheep and to evaluate diet overlap. The aim of our work was to investigate interspecific interactions and to assess the effects of sheep grazing on the summer feeding habits of chamois. A high dietary overlap (Pianka’s index = 0.93–0.99) was found, despite differences in the use of some plant groups. Sheep presence strongly affected chamois feeding habits: a reduction of highly digestible forbs was observed in the chamois diet during August, when both species grazed in the same range. As a consequence of sheep grazing, chamois may have been forced to reduce niche breadth and to change their food habits, increasing percentages of monocotyledons in the diet and feeding mainly on Cyperaceae. The diet overlap between sheep and chamois suggests that resource-mediated interactions as well as direct competition must be taken into account when evaluating chamois and sheep compatibility on Alpine meadows.     

Is the development of infectious keratoconjunctivitis in Alpine ibex and Alpine chamois influenced by topographic features?

Infectious keratoconjunctivitis (IKC) caused by Mycoplasma conjunctivae is a widespread ocular affection of free-ranging Caprinae in the Alpine arc. Along with host and pathogen characteristics, it has been hypothesized that environmental factors such as UV light are involved in the onset and course of the disease. This study aimed at evaluating the role of topographic features as predisposing or aggravating factors for IKC in Alpine chamois (Rupicapra rupicapra rupicapra) and Alpine ibex (Capra ibex ibex). Geospatial analysis was performed to assess the effect of aspect (northness) and elevation on the severity of the disease as well as on the mycoplasmal load in the eyes of affected animals, using data from 723 ibex and chamois (583 healthy animals, 105 IKC-affected animals, and 35 asymptomatic carriers of M. conjunctivae), all sampled in the Swiss Alps between 2008 and 2010. An influence of northness was not found, except that ibex with moderate and severe signs of IKC seem to prefer more north-oriented slopes than individuals without corneal lesions, possibly hinting at a sunlight sensitivity consequent to the disease. In contrast, results suggest that elevation influences the disease course in both ibex and chamois, which could be due to altitude-associated environmental conditions such as UV radiation, cold, and dryness. The results of this study support the hypothesis that environmental factors may play a role in the pathogenesis of IKC.     

Application of DNA fingerprinting to population study of chamois (Rupicapra rupicapra)

Hypervariable minisatellite DNA probes 33.15 and 33.6, originally developed for studies in human populations, were used to study genetic variation in chamois (Rupicapra rupicapra). The mean number of bands per individual was 25 for probe 33.15 and 15 for probe 33.6. The average band frequency was 0.33 for both probes. The mean similarity was 0.44, greater than that reported for human and natural populations and close to values found in domestic populations of mammals. This lack of variability could be related to the bottleneck suffered by the population due to large-scale hunting after the Spanish Civil War. Levels of variability are high compared with variability at the level of protein markers, so the use of minisatellite DNA is recommended for future population studies in this species. We did not find large genetic differences between subpopulations, indicating that the population is genetically homogeneous.     

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.