Comparative survey of gastrointestinal parasites in sympatric Iberian ibex (Capra pyrenaica) and domestic goats using molecular host specific identification.

An isolated population of several hundred Iberian ibex (Capra pyrenaica) inhabits the Gerês-Xurés Transboundary Biosphere Reserve (GXTBR) in north-western Iberian Peninsula, in partial sympatry with tens of thousands domestic goats (Capra hircus). This study aimed to assess the prevalence and shedding intensity of gastrointestinal parasites from sympatric herds of domestic goat and Iberian ibex in autumn 2018. A total of 93 pooled faecal samples were collected from GXTBR (39 from domestic goats and 54 from Iberian ibex) and the host species was identified using molecular techniques, whenever defecation was not visualised in the field. Parasitological analysis was achieved by joint Willis flotation/sedimentation, McMaster and Mini-FLOTAC techniques. Seventy-two samples (25 domestic goats and 47 Iberian ibex) were retained for analysis after discarding the least fresh and those with uncertain specific identification. Generalized linear mixed models compared prevalence and shedding intensity between caprine species. Domestic goats showed a non-significant tendency to be more parasitized than Iberian ibex, as assessed by overall prevalence (100.0%, CI95 86.7-100.0 vs. 74.5%, CI95 69.5-84.8), and shedding intensity. This study reveals a similar community of gastrointestinal parasites in an abundant livestock species and an isolated population of wild caprine, living in partial sympatry. It is the first study on the health status of this endangered Iberian ibex population, in close contact with livestock, highlighting the need for further sanitary surveillance.

Habitat predicts local prevalence of migratory behaviour in an alpine ungulate.

The resource hierarchy hypothesis predicts that the most important factors limiting a species' distribution act at the coarsest spatial scales. However, resource selection behaviour affords mobile organisms the opportunity to adopt a range of tactics for navigating spatial trade-offs between competing biotic and abiotic constraints. Throughout the animal kingdom, partial migration (where some individuals migrate, and others remain resident year round) offers a pervasive example of such behavioural polymorphism. Identifying the differences between these behaviours is therefore central to understanding the conditions (habitat) needed to sustain migrant and resident populations. Here we test an extension of the resource hierarchy hypothesis. We hypothesized that rather than responding to a single limiting factor, migration and residency represent contrasting scale-specific approaches to managing trade-offs between forage, predation risk and severe winter conditions. Furthermore, we predicted that the distribution of habitat selected by migrants and residents is predictive of the local prevalence of migratory behaviour. To test these hypotheses, we quantified migratory status- (resident/migrant) and season-specific (winter/summer) differences in resource selection by eight populations of federally endangered Sierra Nevada bighorn sheep Ovis canadensis sierrae across three spatial scales: population range, individual range and within individual range. We then integrated these spatial predictions to produce separate spatial predictions of migrant and resident winter habitat. As predicted, model selection provided strong evidence for the importance of status-specific differences in resource selection. Residents showed stronger coarse-scale selection for terrain associated with predator avoidance and stronger fine-scale selection for greenness, while in migrants this pattern was reversed. Availability of migrant habitat predicted the local prevalence of migration (top model pseudo R2 of .87). Our ability to respond to global declines of migratory species depends on improving our understanding of the conditions required to maintain migratory behaviour. Through explicitly contrasting migrant and resident behaviour, our results illustrate seasonal differences in migrant and resident habitat and how these two behaviours represent responses to different limiting conditions. Our analyses provides a novel empirical basis for assessing the local prevalence of migratory behaviour across large landscapes.

Surveillance of Sarcoptic Mange in Iberian Ibexes (Capra pyrenaica) and Domestic Goats (Capra hircus) in Southern Spain.

Sarcoptic mange is a highly contagious skin disease caused by Sarcoptes scabiei. Sera were collected from 411 Iberian ibexes, comprising 157 individuals with sarcoptic mange skin lesions and 254 clinically healthy animals, in 13 population nuclei across Andalusia (southern Spain) between 2015 and 2021. Skin samples from 88 of the 157 animals with mange-compatible lesions were also obtained. Moreover, 392 serum samples from domestic goats (Capra hircus) were collected in the same region and study period. Antibodies against S. scabiei were tested using an in-house indirect ELISA, while the presence of mites of S. scabiei was evaluated in the skin samples by potassium hydroxide digestion. Seropositivity was found in eight (3.1%) of the clinically healthy ibexes and in 104 (66.2%) of the animals with mange-compatible lesions. The presence of S. scabiei was confirmed in 57 (64.8%) out of the 88 skin samples analysed and anti-S. scabiei antibodies were found in 49 (86.0%) of these 57 mite-positive individuals. Seropositive animals were detected in population nuclei with previous records of sarcoptic mange, where S. scabiei mites were detected by potassium hydroxide digestion in individuals with sarcoptic mange-compatible external lesions. However, seropositivity was not observed in population nuclei that were historically free of this disease. None of the 392 domestic goats had antibodies against S. scabiei, suggesting an independent epidemiological cycle of sarcoptic mange in Iberian ibex populations in the study area, and a limited or null role of domestic goats in the transmission of the parasite to this wild species. Overall, our findings underscore the importance of maintaining and/or implementing integrated surveillance programs and control strategies in wildlife and livestock, to limit the risk of S. scabiei circulation in Iberian ibex populations.

Evolution of Endogenous Retroviruses in the Subfamily of Caprinae.

The interest in endogenous retroviruses (ERVs) has been fueled by their impact on the evolution of the host genome. In this study, we used multiple pipelines to conduct a de novo exploration and annotation of ERVs in 13 species of the Caprinae subfamily. Through analyses of sequence identity, structural organization, and phylogeny, we defined 28 ERV groups within Caprinae, including 19 gamma retrovirus groups and 9 beta retrovirus groups. Notably, we identified four recent and potentially active groups prevalent in the Caprinae genomes. Additionally, our investigation revealed that most long noncoding genes (lncRNA) and protein-coding genes (PC) contain ERV-derived sequences. Specifically, we observed that ERV-derived sequences were present in approximately 75% of protein-coding genes and 81% of lncRNA genes in sheep. Similarly, in goats, ERV-derived sequences were found in approximately 74% of protein-coding genes and 75% of lncRNA genes. Our findings lead to the conclusion that the majority of ERVs in the Caprinae genomes can be categorized as fossils, representing remnants of past retroviral infections that have become permanently integrated into the genomes. Nevertheless, the identification of the Cap_ERV_20, Cap_ERV_21, Cap_ERV_24, and Cap_ERV_25 groups indicates the presence of relatively recent and potentially active ERVs in these genomes. These particular groups may contribute to the ongoing evolution of the Caprinae genome. The identification of putatively active ERVs in the Caprinae genomes raises the possibility of harnessing them for future genetic marker development.

Description of Gut Mycobiota Composition and Diversity of Caprinae Animals.

The fungal community, also known as mycobiota, plays pivotal roles in host nutrition and metabolism and has potential to cause disease. However, knowledge of the gut fungal structure in Caprinae is quite limited. In this study, the composition and diversity of the gut mycobiota of Caprinae animals from different geographical locations (Anhui, Jilin, Guangxi, Shandong, Shanxi, and Tibet) were comprehensively characterized by analyzing the internal transcribed spacer 2 (ITS-2) sequences of the fungal community. The results showed that Ascomycota and Basidiomycota were the dominant phyla, which, respectively, accounted for 90.86 to 95.27% and 2.58 to 7.62% of sequences in samples from each region. Nonetheless, the structure of the gut mycobiota was largely different in Caprinae animals in the different provinces. Therein, Sporormiaceae and Thelebolaceae were the dominant fungal families in the samples from Tibet, whereas their abundance was generally low in other regions. The intestinal diversity of individuals from Guangxi was higher than that in other regions. In addition, there were 114 differential genera among all regions. Finally, the co-occurrence network revealed 285 significant correlations in cross-family pairs in the guts of Caprinae animals, which contained 149 positive and 136 negative relationships, with 96 bacterial and 86 fungal participants at the family level. This study has improved the understanding of the mycobiota of ruminants and provided support for the improvement in animal health and productivity. IMPORTANCE In this study, we elucidated and analyzed the structure of the gut mycobiota of Caprinae animals from different regions. This study revealed differences in the structure of the gut mycobiota among Caprinae animals from different geographical environments. Based on previous findings, correlations between fungal and bacterial communities were analyzed. This study adds to previous research that has expanded the present understanding of the gut microbiome of Caprinae animals.

Economic Valuation of Balkan Chamois Conservation.

The Balkan chamois (Rupicapra rupicapra balcanica) is a caprine of the rocky mountain slopes, threatened in Greece by illegal hunting and population isolation. We used a contingent valuation method to assess the willingness to pay (WTP) for chamois conservation of 500 residents of the region of Eastern Macedonia and Thrace. Most of the participants (61.6%) were WTP a mean of EUR 41.6 for chamois conservation, totaling EUR 6.03 million for the target population. Attitudes toward and knowledge about chamois, moralistic worldviews (spiritual reverence and ethical concern for nature and wildlife), participation in wildlife-related consumptive outdoor activities (i.e., hunting and fishing), intention to participate in conservation actions for the species, and encounters with the species in the wild were positively associated with WTP for its conservation. Dominionistic worldviews (humans have mastery, physical control, and dominance of wildlife) were negatively associated with WTP, while highly educated females with high income were more WTP for implementing relevant conservation actions. Factors involving previous knowledge of the chamois positively influenced the WTP, thus, confirming the construct's bias toward charismatic species. The findings show that Greek residents highly value the chamois and its conservation and would be useful for advising this process and achieving its conservation management.

The Study of Mechanical Behaviors of Caprinae Horn Sheath under Pendulum Impact.

As a light-weight natural keratin biocomposite, Bovidae horn exhibits high mechanical properties and energy absorption. Different to the widely studied horn from subfamily Bovinae and Antilocapridae, few studies have focused on the horn sheath of subfamily Caprinae. In this work, three Caprinae horn sheathes from Cashmere goat, White goat and Black sheep were selected. Charpy pendulum impact tests were performed, and the fracture characteristics were evaluated. It was demonstrated that water plays an important role in acquiring balanced dynamic mechanical properties in all Caprinae horn sheaths. The hydrated keratin provides large plastic deformation capacity and further gives rise to a gradual generation of micro-cracks. Multi-scale structure including wavy-shaped interface, scattered voids and hierarchical micro-fibre were observed. Such a structure induced complex fracture mechanisms, such as delamination, 90° crack deflection and fibre pull-out, which were probably influenced by interfacial strength. The results are expected to endow the research and thinking of Bovidae horn.

Description of a Sarcoptic Mange Outbreak in Alpine Chamois Using an Enhanced Surveillance Approach.

Since 1995, the Alpine chamois (Rupicapra r. rupicapra) population of the Dolomites has been affected by sarcoptic mange with considerable management concerns. In this study, 15 years (2006-2020) of passive surveillance and demographic data were analyzed in order to describe a mange outbreak. Furthermore, an enhanced passive surveillance protocol was implemented in order to evaluate the efficiency of ordinary vs. enhanced surveillance protocol in identifying dead chamois in the field and in reaching a correct diagnosis. Our results confirm the role of mange as a determining factor for chamois mortality, while stressing the importance of a wider view on the factors affecting population dynamics. The enhanced passive surveillance protocol increased the probability of carcass retrieval and identification of the cause of death; however, its adoption may be too costly if applied for long periods on a wide scale. Passive surveillance, in both ordinary and enhanced surveillance protocol, should encompass the use of other strategies in the future to study the eco-epidemiology of the disease in wild Caprinae.

A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota.

Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.

OCCURRENCE OF FOOTROT IN FREE-RANGING ALPINE IBEX (CAPRA IBEX) COLONIES IN SWITZERLAND.

Footrot is a worldwide economically important, debilitating disease caused by Dichelobacter nodosus. In sheep (Ovis aries), it is characterized by lesions of varying severity, depending on the strain, whereas Alpine ibex (Capra ibex) seem to develop severe lesions, whatever the strain. Healthy carriers occur in livestock but are rare in wild ruminants. Using a triangulation approach (retrospective questionnaire survey, necropsy database screening, and pathogen prevalence estimation in selected ibex colonies with and without footrot), we aimed at evaluating the importance of footrot in the ibex population, identifying potential risk factors for disease occurrence in this species, and defining the epidemiological role of ibex. Our study revealed that footrot occurs throughout the entire ibex territory (34% of the Swiss ibex colonies affected) but only as a sporadic disease (mostly one case per disease event), although the situation differed among footrot-positive colonies because half of them had experienced outbreak recurrences. Risk factor analysis for the occurrence of footrot in ibex colonies suggested an absence of an effect of meteorologic conditions, region, contacts with sheep or cattle (known to be very common healthy carriers of D. nodosus) and existing local disease control program. We found a significant effect only of contacts with sheep having footrot. Pathogen prevalence was very low in all investigated colonies. In conclusion, our results support previous data suggesting that ibex are susceptible spillover hosts, likely infected mainly by sympatric sheep displaying clinical signs.

Analysis of gut microbiota in three species belonging to different genera (Hemitragus, Pseudois, and Ovis) from the subfamily Caprinae in the absence of environmental variance.

This study aimed to identify the effects of host species on the gut microbial flora in three species (Hemitragus jemlahicus, Pseudois nayaur, and Ovis orientalis) from the subfamily Caprinae, by excluding the impact of environment factors. We investigated the differences in intestinal flora of three species belonging to Caprinae, which were raised in identical conditions. Fecal samples were collected from tahr, mouflon, and bharal, and the V3-V4 region of the 16S ribosomal RNA gene was analyzed by high-throughput sequencing. The analysis of 16S rRNA gene sequences reveals that fecal samples were mainly composed of four phyla: Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria. The most abundant phyla included Firmicutes and Bacteroidetes accounting for >90% of the bacteria, and a higher Firmicutes/Bacteroidetes ratio was observed in tahrs. Moreover, significant differences existed at multiple levels of classifications in the relative abundance of intestinal flora, differing greatly between species. Phylogenetic analyses based on 16S rRNA gene indicated that mouflon is closely related to bharal, and it is inconsistent with previous reports in the species evolutionary relationships. In this study, we demonstrated that the gut microbiota in tahr had a stronger ability to absorb and store energy from the diet compared with mouflon and bharal, and the characteristics of host-microbiome interactions were not significant.

Complete mitochondrial genomes of Karchaev goat (Capra hircus).

Karachaev goat (Capra hircus) is a local breed from North-Caucasus region, Russia. Here we present complete mitochondrial genome of Karachaev goat from the republic of Karachaevo-Cherkessia, Russia. The length of the studied sequence was 16,624 bp in size. It was shown that the studied specimen belonged to haplogroup A.

Sarcoptic Mange in Wild Caprinae of the Alps: Could Pathology Help in Filling the Gaps in Knowledge?

Sarcoptic mange represents the most severe disease for wild Caprinae individuals and populations in Europe, raising concerns for both conservation and management of these ungulates. To date, this disease has been investigated in different wild caprine species and under many different perspectives including diagnostics, epidemiology, impact on the host populations, and genetics of both hosts and parasite, with the aim to disentangle the host-Sarcoptes scabiei relationship. Notwithstanding, uncertainty remains and basic questions still need an answer. Among these are the effect of immune responses on mange severity at an individual level, the main drivers in host-parasite interactions for different clinical outcomes, and the role of the immune response in determining the shift from epidemic to endemic cycle. A deeper approach to the pathology of this disease seems therefore advisable, all the more reason considering that immune response to S. scabiei in wild Caprinae, generally classified as a hypersensitivity, remains poorly understood. In this paper, we reviewed the pathological features associated to sarcoptic mange in wildlife, exploring different kinds of hypersensitivity and outcomes, with the objective of highlighting the major drivers in the different responses to this disease at an individual level and proposing some key topics for future research, with a particular attention to Alps-dwelling wild caprines.

Genome Assembly and Analysis of the North American Mountain Goat (Oreamnos americanus) Reveals Species-Level Responses to Extreme Environments.

The North American mountain goat (Oreamnos americanus) is an iconic alpine species that faces stressors from climate change, industrial development, and recreational activities. This species' phylogenetic position within the Caprinae lineage has not been resolved and their phylogeographic history is dynamic and controversial. Genomic data could be used to address these questions and provide valuable insights to conservation and management initiatives. We sequenced short-read genomic libraries constructed from a DNA sample of a 2.5-year-old female mountain goat at 80X coverage. We improved the short-read assembly by generating Chicago library data and scaffolding using the HiRise approach. The final assembly was 2,506 Mbp in length with an N50 of 66.6 Mbp, which is within the length range and in the upper quartile for N50 published ungulate genome assemblies. Comparative analysis identified 84 gene families unique to the mountain goat. The species demographic history in terms of effective population size generally mirrored climatic trends over the past one hundred thousand years and showed a sharp decline during the last glacial maximum. This genome assembly will provide a reference basis for future population and comparative genomic analyses.

Conservation, Divergence, and Functions of Centromeric Satellite DNA Families in the Bovidae.

Repetitive satellite DNA (satDNA) sequences are abundant in eukaryote genomes, with a structural and functional role in centromeric function. We analyzed the nucleotide sequence and chromosomal location of the five known cattle (Bos taurus) satDNA families in seven species from the tribe Tragelaphini (Bovinae subfamily). One of the families (SAT1.723) was present at the chromosomes' centromeres of the Tragelaphini species, as well in two more distantly related bovid species, Ovis aries and Capra hircus. Analysis of the interaction of SAT1.723 with centromeric proteins revealed that this satDNA sequence is involved in the centromeric activity in all the species analyzed and that it is preserved for at least 15-20 Myr across Bovidae species. The satDNA sequence similarity among the analyzed species reflected different stages of homogeneity/heterogeneity, revealing the evolutionary history of each satDNA family. The SAT1.723 monomer-flanking regions showed the presence of transposable elements, explaining the extensive shuffling of this satDNA between different genomic regions.

The complete mitochondrial genome sequence of the Himalayan goral, Naemorhedus goral (Cetartiodactyla: Caprinae).

The Himalayan goral (Naemorhedus goral) belongs to the subfamily Caprinae, which is distributed across the Himalayas including Bhutan, northern India including Sikkim and Arunachal Pradesh, Nepal, southern Tibet, and possibly western Myanmar. In this study, the complete mitochondrial genome of N. goral was sequenced. The mitogenome was 16 533 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the N. goral is 33.7% A, 27.2% T, 26.0% C, and 13.1% G. Phylogenetic analysis based on the mitogenome sequences using the Bayesian inferences method showed that Naemorhedus and Capricornis formed a monophyletic group and the N. goral was closely related to N. griseus. We expect that the present results will facilitate further investigation of the phylogenetic relationships and population genetics of genus Naemorhedus.

Complete mitochondrial genome of red goral (Naemorhedus baileyi) and a complete estimate of the phylogenetic relationships in Caprinae.

Naemorhedus baileyi belongs to the genera Naemorhedus within the subfamily Caprinae. Because of small population, narrow distribution and difficult sampling, the taxonomic status of red goral in Caprinae is still not clear. We extracted the sample DNA and amplified whole mtDNA genome with different primers. We downloaded other gene sequences of Caprinae from GenBank. All sequences included 24 species of 11 genera. Phylogenetic analyses confirmed that the subfamily Caprinae is not monophyletic, bootstrap support for this cluster is high (100%).

The complete mitochondrial genome sequence of the Chinese Serow, Capricornis milneedwardsii (Cetartiodactyla: Caprinae).

The Chinese Serow (Capricornis milneedwardsii) is a native species distributed in China and Southeast Asia, and has been listed as one of the Class II national protected species in China. Here we first determined and annotated its complete mitochondrial genome. The mito-genome of Chinese Serow is 16,444 bp in length, consisting of two ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, 13 protein-coding genes, and one control region. The overall base composition is A: 33.5%, T: 26.7%, C: 26.6%, and G: 13.2%, with a much higher A + T content.

Complete mitochondrial genome sequence of the blue sheep, Pseudois nayaur szechuanensis (Cetartiodactyla: Caprinae).

The blue sheep (Pseudois nayaur szechuanensis) belongs to the subfamily Caprinae, which distributes in Sichuan, Gansu, Qinghai, southeastern Xinjiang, northern Yunnan and Ningxia-Inner Mongolia border, China. In this study, the complete mitochondrial genome of P. n. szechuanensis was sequenced. The mitogenome was 16,738 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a non-coding control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes which are encoded on the light strand. The overall base composition of the P. n. szechuanensis is 33.5% A, 26.4% T, 27.0% C, and 13.2% G. The alignment of the Pseudois species control regions exhibited high genetic variability and rich A + T content. The complete mitogenome of P. n. szechuanensis can provide an important data for the studies on phylogenetic relationship and population genetics to further explore the taxonomic status of this species.

Complete mitochondrial genome of a new subspecies of the blue sheep, Pseudois nayaur (Cetartiodactyla: Caprinae) from Helan Mountain in China.

The population of blue sheep, Pseudois nayaur, from Helan Mountain in China is considered as a new subspecies. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,795 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.2%, T: 26.6%, C: 26.8% and G: 13.3%. The complete mitogenome of the new subspecies of P. nayaur could provide an important data to further explore the taxonomic status of the subspecies.