Cytochrome b pseudogene originated from a highly divergent mitochondrial lineage in genus Rupicapra

We have identified a nuclear pseudogene (numt) of cytochrome b (cytb) in chamois. The comparison of a fragment of 402 nucleotides of cytb and the pseudogene between the 2 species Rupicapra rupicapra and Rupicapra pyrenaica allowed direct measurement of relative rates and patterns of evolution. Mitochondrial genes evolved 7 to 12 times faster than their nuclear counterparts. Substitutions in the nucleus include a frameshift and a stop codon. Phylogenetic analysis of nuclear and mitochondrial lineages on Rupicapra and related species showed that the nuclear branch evolved as a functional mitochondrial gene until the split of the 2 species of chamois and as a typical pseudogene later on. We propose that the pseudogene originated from a highly divergent mitochondrial lineage that did not persist in the mitochondrion and transposed to the nucleus in a time close to speciation. The concurrence of highly differentiated lineages at speciation points to hybridization between highly divergent populations.     

The conservation of the chamois Rupicapra spp.

• 1 Despite it being the most abundant mountain dwelling ungulate of Europe and the Near East, the taxonomy, systematics and biology of the chamois are still imperfectly known. Although neither species of chamois is at risk, several subspecies are threatened (Rupicapra rupicapra cartusiana, Rupicapra rupicapra tatrica and Rupicapra rupicapra balcanica; Rupicapra pyrenaica ornata. Rupicapra rupicapra asiatica is data‐deficient but probably threatened).
• 2 A life history with apparently contradictory relationships between survival, sexual dimorphism and mating system suggests a unique survival strategy not yet fully understood. Over the last century, morphologic, biometric, behavioural and genetic features have been studied to shed light on the phylogeography and monophyly or polyphyly of the chamois as well as on the number of existing species and subspecies of the genus Rupicapra.
• 3 The dispersal hypothesis, according to which R. rupicapra migrated westward from eastern Europe in the Quaternary, confining R. pyrenaica to the southernmost regions of Europe, has been recently called into question by some molecular analyses that yielded contradictory results.
• 4 In spite of subtleties relevant to each method of analysis, an overall evaluation of differences between the R. rupicapra and the R. pyrenaica groups strongly supports the functional separation of the taxa into two species.
• 5 Further studies on the ecology of chamois, as well as on the epidemiology of severe diseases, e.g. sarcoptic mange, are needed to improve the management of viable populations.
• 6 Before translocations and reintroductions are carried out, the risk of hybridization leading to genetic extinction should be evaluated.

     

Late Pleistocene and Holocene chamois in Italy

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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.     

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.     

Diffusion of pulmonary Nematoda in the steinbock (Capra ibex) and the chamois (Rupicapra rupicapra) at the Gran Paradiso National Park and the di Valdieri Reservation]

The results obtained in a survey on the diffusion of pulmonary nematodes in 13 steinbocks (Capra ibex) and 71 chamois (Rupicapra rupicapra) of the Parco Nazionale del Gran Paradiso, and 49 chamois of the Riserva di Valdieri, Italian Western Alps, are reported. The following species of nematodes were identified: Spiculocaulus austriacus, Protostrongylus rufescens, Protostrongylus hobmaieri in steinbocks; Protostrongylus rupicaprae, Protostrongylus hobmaieri, Protostrongylus refescens,Protostrongylus sp., Spiculocaulus austriacus and Dictyocaulus filaria in chamois. The study of two species, viz. Spiculocaulus austriacus and Protostrongylus sp., is still in progress because these nematodes show morphological peculiarities never previously described.     

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 (deltamu)(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.     

Isolation of Brucella melitensis biovar 3 from a chamois (Rupicapra rupicapra) in the southern French Alps

Systemic brucellosis caused by Brucella melitensis biovar 3 was identified in a chamois (Rupicapra rupicapra) near the Parc National des Ecrins in the southern French Alps (France). Clinical signs included orchiepididymitis, polyarthritis, blindness and various neurological signs; necropsy findings included numerous calcified foci in testis, epididymis, kidney, subcutaneous connective tissue and brain. Brucella sp. were identified in brain by indirect immunofluorescence and B. melitensis biovar 3 was isolated from testis, kidney, eye, lung and joints. This report describes the first case of brucellosis and Brucella sp. isolation in chamois in France and the first case of B. melitensis isolation in this host species.     

Interspecific and seasonal dietary differences of Himalayan thar, chamois and brushtail possums in the central Southern Alps, New Zealand

Himalayan thar or tahr (Hemitragus jemlahicus), Alpine chamois (Rupicapra rupicapra) and brushtail possums (Trichosurus vulpecula) are native to the Himalaya, Europe and Australia, respectively, but are now sympatric in parts of the central Southern Alps, New Zealand. All three species are managed as pests by the Department of Conservation. We analysed the diets of 246 thar, 78 chamois and 113 possums collected in the central Southern Alps during 1988–1996. The diets of thar and chamois strongly overlapped, but thar ate more grasses and less herbs and woody plants than chamois. The diet of possums differed from the diets of thar and chamois, containing a different suite of herbs and almost no grasses. The diets of thar, chamois and possums varied seasonally. Contrary to expectation, the diets of adult male and female thar were similar during the period when they are spatially segregated (October–May). Chamois sampled outside the thar range ate more species than those sampled inside the thar range, suggesting that the presence of thar modifies the diet of chamois. If managers wish to protect the dominant Chionochloa snow tussocks then thar should be controlled; chamois should be controlled to protect herbs such as Ranunculus spp.; and possums should be controlled if Podocarpus nivalis or Muehlenbeckia axillaris need to be protected. However, managers need to be aware of the potential for chamois to increase in abundance, at least in some sites, if thar are controlled to low abundance, and that this could lead to different impacts on plant populations.     

Phylogeography of roe deer (Capreolus capreolus) populations: the effects of historical genetic subdivisions and recent nonequilibrium dynamics

We sequenced 704 mitochondrial DNA (mtDNA) control-region nucleotides and genotyped 11 autosomal microsatellites (STR) in 617 European roe deer (Capreolus capreolus) samples, aiming to infer the species' phylogeographical structure. The mtDNA sequences were split in three distinct haplogroups, respectively, named: Clade West, sampled mainly in Iberia; Clade East, sampled mainly in Greece and in the Balkans; and Clade Central, which was widespread throughout Europe, including the eastern countries and Iberia, but not Greece. These clades might have originated in distinct Iberian and Balkanic refuges during the penultimate or the last glaciations. Clades East and West contributed little to the current postglacial mtDNA diversity in central Europe, which apparently was recolonized mainly by haplotypes belonging to Clade Central. A unique subclade within Clade Central grouped all the haplotypes sampled from populations of the Italian subspecies C. c. italicus. In contrast, haplotypes sampled in central and southern Spain joined both Clade Central and Clade West, suggesting that subspecies C. c. garganta has admixed origin. STR data support a genetic distinction of peripheral populations in north Iberia and southern Italy, and show the effects of anthropogenic disturbance in fragmented populations, which were recently reintroduced or restocked and not may be in mutation-drift equilibrium. Roe deer in central Europe are mainly admixed, while peripheral populations in north Portugal, the southern Italian Apennines and Greece represent the remains of refugial populations and should be managed accordingly.     

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.     

Serosurvey of roe deer, chamois and domestic sheep in the central Italian Alps

Roe deer (Capreolus capreolus), chamois (Rupicapra rupricapra rupicapra), and domestic sheep in the Orobie Alps, Italy, were serologically tested for antibodies to selected pathogens that may be transmitted across species. Antibodies against Brucella spp. and bovine herpesvirus 1 (roe deer and chamois only) were not detected in any species. In roe deer, antibodies were detected against Toxoplasma gondii (13%) and Neospora caninum (3%). Chamois tested positive for antibodies to T. gondii (5%), N. caninum (21%), bovine respiratory syncytial virus (BRSV) (41%), bovine parainfluenza type-3 virus (17%), pestiviruses (18%), and Mycoplasma conjunctivae (17%). In the sheep, particularly high antibody prevalence rates were found for T. gondii (78%), Chlamydophila spp. (20%), pestiviruses (90%), BRSV (82%), and M. conjunctivae (81%).     

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.     

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.     

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.

     

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.     

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.     

Verocytotoxin-producing Escherichia coli in chamois (Rupicapra rupicapra) and cattle in Austria

We assessed the prevalence of verotoxigenic Escherichia coli (VTEC) in chamois (Rupicapra rupicapra) and livestock grazing on a mountain pasture in Austria during June-August 2009. We detected VTEC throughout the sampling period in high numbers in cattle as well as in chamois, leading to the assumption that the degree of contamination of the environment is high. This is the first report of pathogenic E. coli identified in chamois, implicating chamois as a new potential reservoir of these zoonotic pathogens. Because the study area also serves recreational purposes, there is a risk of humans acquiring infection via direct or indirect contact.     

Spatial patterns of mitochondrial and nuclear gene pools in chamois (Rupicapra r. rupicapra) from the Eastern Alps

We have assessed the variability of maternally (mtDNA) and biparentally (allozymes) inherited genes of 443 chamois (Rupicapra r. rupicapra) from 19 regional samples in the Eastern Alps, to estimate the degree and patterns of spatial gene pool differentiation, and their possible causes. Based on a total mtDNA-RFLP approach with 16 hexanucleotide-recognizing restriction endonucleases, we found marked substructuring of the maternal gene pool into four phylogeographic groups. A hierarchical AMOVA revealed that 67.09% of the variance was partitioned among these four mtDNA-phylogroups, whereas only 8.04% were because of partitioning among regional samples within the populations, and 24.86% due to partitioning among individuals within regional samples. We interpreted this spatial pattern of mtDNA variability as a result of immigration of chamois from different Pleistocene refugia surrounding the Alps after the withdrawal of glaciers, rather than from topographic barriers to gene flow, such as Alpine valleys, extended glaciers or woodlands. However, this striking geographical structuring of the maternal genome was not paralleled by allelic variation at 33 allozyme loci, which were used as nuclear DNA markers. Wright's hierarchical F-statistics revealed that only < or =0.45% of the explained allozymic diversity was because of partitioning among the four mtDNA-phylogroups. We conclude that this discordance of spatial patterns of nuclear and mtDNA gene pools results from a phylogeographic background and sex-specific dispersal, with higher levels of philopatry in females.