Bezoar (Capra aegagrus) Is a Matriarchal Candidate for Ancestor of Domestic Goat (Capra hircus): Evidence from the Mitochondrial DNA Diversity

The leading hypothesis on the ancestor of domestic goats (Capra hircus) is that it is the wild goat called the bezoar or pasang (Capra aegagrus). To verify this hypothesis, we sequenced and compared the cytochrome b gene of mitochondrial DNA from six domestic goats and a bezoar. A further sequence for the markhor was taken from the database. In total we detected 51 nucleotide substitutions among the domestic goats, bezoar and markhor. However, only one specific nucleotide substitution was found between the domestic goats and the bezoar. On the other hand, 43 nucleotide substitutions were specific for the markhor. This result suggested a close relationship between the domestic goats and the bezoar. A neighbor-joining and parsimony phylogenetic tree constructed using the sequences showed that the domestic goats and the bezoar belong to the same cluster, while the markhor showed a distinct cluster separate from that of the domestic/bezoar cluster. This result was confirmed by trees based on the sequence of the mitochondrial displacement loop regions. These results suggest that the strongest candidate for a matriarchal ancestor of domestic goats is the bezoar.     

Evidence for Introgressive Hybridization of Captive Markhor (Capra falconeri) with Domestic Goat: Cautions for Reintroduction

Markhors (Capra falconeri) are among the most endangered mammal species, and several conservation measures, including ex situ breeding, are implemented to prevent their extinction. We studied sequence diversity and differentiation of the first hypervariable segment of the mitochondrial DNA control region among C. f. heptneri and C. f. megaceros kept in four zoos in relationship to lineages of other wild and domestic goats, to assess for the first time the level of molecular distinctness and variability among those subspecies, and to check for possible introgression by related Capra taxa, such as domestic goats. Levels of differentiation between some Capra falconeri lineages and modern domestic goats were similar to levels between other wild goat species (i.e., Capra aegagrus, Capra ibex) and domestic goats. Among pure markhor lineages, paraphyly was observed for C. f. heptneri, suggesting occurrence of shared ancestral polymorphism among markhor subspecies and/or ancient or recent gene exchange between subspecies. Interestingly, 35.7% of all studied markhors from three zoos are introgressed by the domestic goat. Furthermore, despite relatively small breeding group sizes, markhors have maintained a relatively high proportion of mtDNA variation within zoo groups. In any case, the existence of markhors introgressed with domestic goat DNA in zoos should be considered when selecting markhors for ex situ breeding programs with the aim of building up a stock for later reintroduction into the wild.     

Protection of Spanish Ibex (Capra pyrenaica) against Bluetongue virus serotypes 1 and 8 in a subclinical experimental infection

Many wild ruminants such as Spanish ibex (Capra pyrenaica) are susceptible to Bluetongue virus (BTV) infection, which causes disease mainly in domestic sheep and cattle. Outbreaks involving either BTV serotypes 1 (BTV-1) and 8 (BTV-8) are currently challenging Europe. Inclusion of wildlife vaccination among BTV control measures should be considered in certain species. In the present study, four out of fifteen seronegative Spanish ibexes were immunized with a single dose of inactivated vaccine against BTV-1, four against BTV-8 and seven ibexes were non vaccinated controls. Seven ibexes (four vaccinated and three controls) were inoculated with each BTV serotype. Antibody and IFN-gamma responses were evaluated until 28 days after inoculation (dpi). The vaccinated ibexes showed significant (P<0.05) neutralizing antibody levels after vaccination compared to non vaccinated ibexes. The non vaccinated ibexes remained seronegative until challenge and showed neutralizing antibodies from 7 dpi. BTV RNA was detected in the blood of non vaccinated ibexes from 2 to the end of the study (28 dpi) and in target tissue samples obtained at necropsy (8 and 28 dpi). BTV-1 was successfully isolated on cell culture from blood and target tissues of non vaccinated ibexes. Clinical signs were unapparent and no gross lesions were found at necropsy. Our results show for the first time that Spanish ibex is susceptible and asymptomatic to BTV infection and also that a single dose of vaccine prevents viraemia against BTV-1 and BTV-8 replication.     

Epidemiology of Mycoplasma agalactiae infection in free-ranging Spanish ibex (Capra pyrenaica) in Andalusia, southern Spain

Mycoplasma agalactiae is the main causal agent of contagious agalactia syndrome in Spain. It is a severe disease of small ruminants, endemic in Mediterranean countries, that is characterized by mastitis, arthritis, and keratoconjunctivitis. This paper investigates the temporal, spatial, and host-related factors in the distribution of M. agalactiae infection from October 1996 to November 1998 and March 2002 to May 2003 in Spanish ibex (Capra pyrenaica) populations from Andalusia, in southern Spain. The predisposing factors to infection among previously selected factors (year of sampling, climatic season, geographic origin according to province, mountain range and metapopulation, sex, year of life, presence of scabies, and phase of the reproductive cycle) were established. We collected conjunctival and ear-canal swabs from 411 free-ranging ibexes. The frequency of infected ibexes was 11.2%. The peak frequency of infection occurred in 1998 and in summer. Granada was the province with greatest risk (odds ratio = 2.6) of carriers (18.8% infected). The predisposing factors were sex (females), age (young animals), and metapopulation (Sierra Nevada). We identified a higher number of infected ibexes in the metapopulation "Sierra Nevada" (34/ 256) and significant differences among the three established metapopulations (P<0.01). Mycoplasma agalactiae infection represents a risk for population density and maintenance of these wild populations; infections can result in blindness, malnutrition, and polyarthritis leading to numerous deaths.     

Brucella melitensis in France: Persistence in Wildlife and Probable Spillover from Alpine Ibex to Domestic Animals

Bovine brucellosis is a major zoonosis, mainly caused by Brucella abortus, more rarely by Brucella melitensis. France has been bovine brucellosis officially-free since 2005 with no cases reported in domestic/wild ruminants since 2003. In 2012, bovine and autochthonous human cases due to B. melitensis biovar 3 (Bmel3) occurred in the French Alps. Epidemiological investigations implemented in wild and domestic ruminants evidenced a high seroprevalence (>45%) in Alpine ibex (Capra ibex); no cases were disclosed in other domestic or wild ruminants, except for one isolated case in a chamois (Rupicapra rupicapra). These results raised the question of a possible persistence/emergence of Brucella in wildlife. The purpose of this study was to assess genetic relationships among the Bmel3 strains historically isolated in humans, domestic and wild ruminants in Southeastern France, over two decades, by the MLVA-panel2B assay, and to propose a possible explanation for the origin of the recent bovine and human infections. Indeed, this genotyping strategy proved to be efficient for this microepidemiological investigation using an interpretation cut-off established for a fine-scale setting. The isolates, from the 2012 domestic/human outbreak harbored an identical genotype, confirming a recent and direct contamination from cattle to human. Interestingly, they clustered not only with isolates from wildlife in 2012, but also with local historical domestic isolates, in particular with the 1999 last bovine case in the same massif. Altogether, our results suggest that the recent bovine outbreak could have originated from the Alpine ibex population. This is the first report of a B. melitensis spillover from wildlife to domestic ruminants and the sustainability of the infection in Alpine ibex. However, this wild population, reintroduced in the 1970s in an almost closed massif, might be considered as a semi-domestic free-ranging herd. Anthropogenic factors could therefore account with the high observed intra-species prevalence.     

The Origin and Genetic Status of Insular Caprines in the Eastern Mediterranean: A Case Study of Free-Ranging Goats (Capra aegagrus cretica) on Crete

The history and species status of free-ranging goats inhabiting the Eastern Mediterranean islands is discussed with reference to morphometric, archaeological and genetic findings. A case study on the free-ranging goats on Crete (Capra aegagrus cretica) is presented. The phenotype of the Cretan goat resembles that of the wild bezoar goat (C. aegagrus). However, the mitochondrial DNA of cytochrome b and d-loop sequences shows affinity with domestic goats. It has been suggested that the Cretan goat represents a feral animal that was introduced onto the island during the 6th millennium b.c. as a primitive domestic, and has retained the wild morphotype but has undergone significant genetic change. An alternative explanation, and the one that is proposed here, is that the goat was introduced onto the island in wild form and released as a food source. Subsequent introgressions with domestic animals, especially ewes, have influenced its genotype. These conclusions are applicable to other free-living goats and sheep which inhabit islands in the Eastern Mediterranean.     

Evolutionary history of the genus Capra (Mammalia, Artiodactyla): discordance between mitochondrial DNA and Y-chromosome phylogenies

The systematics of the genus Capra remain controversial in spite of studies conducted using morphology, mtDNA, and allozymes. Here, we assess the evolutionary history of Capra (i) using phylogenetic analysis of two nuclear genes located on the Y-chromosome and (ii) previously published and new cytochrome b sequences. For the Y-chromosome phylogeny, we sequenced segments from the amelogenin (AMELY) and zinc finger (ZFY) genes from all of the eight wild taxa and from domestic goats (Capra hircus). Phylogenetic analysis of the Y-chromosome data revealed two well-defined clades. The domestic goat (C. hircus), the bezoar (Capra aegagrus), and the markhor (C. falconeri) belong to one clade (ML bootstrap value [BP]: 98%), suggesting that domestic goats originated from one or both of these wild species. The second clade (ML BP: 92%) is comprised of all the other wild species. Horn morphology is generally concordant with the Y-chromosome phylogeny. The mtDNA data also revealed two well-defined clades. However, the species in each clade are different from those inferred from the Y-chromosome data. To explain the discordance between Y-chromosome and mtDNA phylogenies, several hypotheses are considered. We suggest that a plausible scenario involves mtDNA introgression between ancestral taxa before the relatively recent colonization of Western Europe, the Caucasus Mountains, and East Africa by Capra populations.     

Mitochondrial DNA Reveal that Domestic Goat (Capra hircus) are Genetically Affected by Two Subspecies of Bezoar (Capra aegagurus)

This article describes the complete sequences of the mitochondrial DNA displacement loop (D-loop) region and cytochrome b gene from domestic goats in Laos (Laos native) and wild goat markhor (C. falconeri). The wild goat bezoar (Capra aegagrus) has been considered to be the strongest candidate for the ancestor of the domestic goats (C. hircus); however, there is not sufficient molecular data to verify the hypothesis at present. In phylogenetic analyses, two wild goats, the markhor and the ibex (C. ibex), appeared as an outgroup, while the bezoar was located in a cluster of domestic goats. Mitochondrial haplotypes of Laos natives revealed two distinct major clusters: one was the same as the bezoar, the second, unique to Laos natives. The topology and calibrated levels of sequence divergence suggests that these clusters might represent at least two different subspecies of ancestral bezoars.     

Serological survey of selected infectious diseases in mouflon (Ovis aries musimon) from south-central Spain

Serum samples from 101 mouflons (Ovis aries musimon) collected from July 2002 to January 2006 were tested for antibodies against Anaplasma spp., Brucella spp., bovine viral diarrhea virus, Chlamydophila abortus, Coxiella burnetii, Mycobacterium avium ssp. paratuberculosis, and Maedi-Visna virus. Mouflon came either from extensive farms or high ungulate density fenced hunting estates. Antibodies were detected against Anaplasma spp. (22.2%), C. burnetii (4.0%), M. avium ssp. paratuberculosis (1.0%) and C. abortus (1.0%). According to our results, mouflons could participate as a wild reservoir in the epidemiology of Anaplasma spp. infection and maybe Q fever, but they do not seem to contribute in the epidemiology of the rest of the studied infectious diseases in south-central Spain.     

Epidemiological studies on caprine arthritis-encephalitis virus infection in Jordan

To investigate the seroprevalence of, and risk factors for, caprine arthritis-encephalitis virus (CAEV) infection in different breeds of goats in Jordan, sera from 1100 goats from three different geographical regions in Jordan were analyzed. Prevalence of antibodies to CAEV was determined using a competitive ELISA test. A semi-structured questionnaire was used to collect information on herd health and management. Questionnaire data were tested in a multivariable logistic regression model to elucidate risk factors associated with CAEV seropositivity. In addition, the incidence of CAEV antibodies was investigated in six goat herds located in the northern part of Jordan. Out of the 69 goat herds investigated, 16 (23.2%) had antibodies against CAEV. Individual goat true seroprevalence to CAEV was 8.9%. The highest CAEV seroprevalence was observed in goats older than 3-years and younger than 6-years of age. The seroprevalence of CAEV in goats was significantly higher (P < 0.05) in the northern part of Jordan than that in central or southern parts of Jordan. The multivariable logistic regression model identified large herd size (OD = 2.0; 95% CI: 1.1, 2.7), addition of new animals to the herd (OD = 1.3; 95% CI: 0.3, 1.6) and contact with other goat herds (OD = 1.1; 95% CI: 0.9, 2.0) as risk factors for CAEV seropositivity. The incidence of CAEV seropositivity in the six herds monitored in the northern part of Jordan ranged from 2.4 to 5.3%.     

Prevalence of antibodies against selected agents shared between Cantabrian chamois (Rupicapra pyrenaica parva) and domestic goats

Southern chamois (Rupicapra pyrenaica) share the habitat with domestic ungulates, and may, therefore, play a role in the epidemiology of shared agents. The objective of this study was to determine the seroprevalence for Brucella spp., Mycobacterium avium ssp. paratuberculosis (MAP), pestivirus, and Sarcoptes scabiei in Cantabrian chamois (Rupicapra pyrenaica parva) and compare these data with those of sympatric domestic goats (Capra hircus). From 2005 to 2008, blood samples were obtained from 236 adult Cantabrian chamois in two different populations, the western one and the eastern one. Seroprevalence for Brucella spp. and pestivirus was assessed using commercial ELISA kits, whereas specifically designed ELISA tests were used for MAP and S. scabiei. No antibodies against Brucella spp. were detected. Conversely, antibodies against MAP, pestivirus (chamois 3.8%; goat 2.3%), and S. scabiei (chamois 11.9%; goat 12.8%) were detected in both species. Seroprevalence for MAP was significantly higher for domestic goats (26%) than for chamois (9.7%). In chamois, seroprevalence for pestivirus was higher in the west (6.5%) than in the east (range 0–1.8%), whereas seroprevalence for S. scabiei followed the opposite trend (west 4.6%; east 16.7–21.4%). We suggest that certain diseases could circulate between Cantabrian chamois and domestic goat populations, and domestic livestock may suppose a threat for the health status of sympatric Cantabrian chamois.     

Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication

Background

Domestic goats (Capra hircus) have been selected to play an essential role in agricultural production systems, since being domesticated from their wild progenitor, bezoar (Capra aegagrus). A detailed understanding of the genetic consequences imparted by the domestication process remains a key goal of evolutionary genomics.

Results

We constructed the reference genome of bezoar and sequenced representative breeds of domestic goats to search for genomic changes that likely have accompanied goat domestication and breed formation. Thirteen copy number variation genes associated with coat color were identified in domestic goats, among which ASIP gene duplication contributes to the generation of light coat-color phenotype in domestic goats. Analysis of rapidly evolving genes identified genic changes underlying behavior-related traits, immune response and production-related traits.

Conclusion

Based on the comparison studies of copy number variation genes and rapidly evolving genes between wild and domestic goat, our findings and methodology shed light on the genetic mechanism of animal domestication and will facilitate future goat breeding.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1606-1) contains supplementary material, which is available to authorized users.     

Disruption of the S41 Peptidase Gene in Mycoplasma mycoides capri Impacts Proteome Profile,H2O2 Production,and Sensitivity to Heat Shock

Members of the Mycoplasma mycoides cluster are among the most virulent of the mycoplasmas, causing worldwide economically significant diseases of cattle and goats. A distinguishing phenotype among the members of the cluster is the ability to degrade casein. The MMCAP2_0241 gene, an S41 peptidase, confers the proteolytic phenotype in Mycoplasma mycoides subsp. capri GM12. In order to determine the impact of disruption of the gene, we used differential proteome profiling to compare the M. mycoides subsp. capri wild type with a mutant lacking the proteolytic phenotype. Disruption of MMCAP2_0241 resulted in altered phenotypes reminiscent of M. mycoides subsp. mycoides SC and had significant impacts on the proteome profile of the microbe. The mutant exhibited increased production of hydrogen peroxide, decreased lactate dehydrogenase activity, and increased sensitivity to heat shock.     

Comparative evaluation of a new commercial recombinant ELISA and the complement fixation test for the diagnosis of Chlamydophila abortus infection in naturally infected flocks in Tunisia

Chlamydiosis is a significant cause of abortion in goats and sheep in Tunisia. A new commercially available ELISA (ELISA-Chlamydophila abortus, ELISA-C. abortus) for detecting antibodies against C. abortus was evaluated using field sheep and goat serum samples. This ELISA is based on a recombinant antigen that expresses part of a protein from 80 to 90 kDa family that is specific to C. abortus. Serum samples collected from 219 sheep and 53 goats flock presenting abortion problems were used in this study. To assess the sensitivity of this new serological test, it was compared with the complement fixation test (CFT) using ELISA-antigen (Elisa-ag) detection and/or isolation as reference technique. Only 61.1% of the sera gave concordant results in both ELISA-C. abortus and CFT, and results were non-concordant for 22.4% due to 16.5% of doubtful results on CFT. The concordance of ELISA-C. abortus and Elisa-ag result was 65% while that of the CFT with ELISA-antigen was only 45%. This study using field material demonstrated that ELISA-C. abortus is a suitable method for diagnosis of chlamydiosis in order to implement early prophylactic measures from the first cases of abortion, both to stop the spread of infection and to prevent associated economic loss.     

Caprine mycoplasmal mastitis in Nigeria

In a study to investigate the current status of intramammary mycoplasmosis in caprine udders in Nigeria, a total of 57 and 24 milk samples were collected from udders of goats affected by mastitis and from apparently normal goats’ udders, respectively. Acute and chronic mastitis were more commonly observed in goats between 1 and 3 years old. Mycoplasma agalactiae and Mycoplasma capricolum occurred at a significantly higher rate (p<0.05) in udders affected by mastitis than in normal healthy udders. Other mycoplasma occurring in low prevalence include Mycoplasma bovis and Mycoplasma mycoides subsp. mycoides LC. It is concluded that cultural (microbiological) surveillance is necessary for effective treatment and control of the disease in Nigeria.     

Chlamydophila abortus in a Brown Skua (Catharacta antarctica lonnbergi) from a Subantarctic Island

On Bird Island, South Georgia, a new strain of Chlamydophila abortus was detected in one Brown skua out of 37 specimens from six different seabird species. Phylogenetic analysis of the rnpB and omp1 genes indicated the strain to be more closely related to C. abortus than to 6BC, the type strain of Chlamydophila psittaci.     

Comparative genomics analysis of Mycoplasma capricolum subsp. capripneumoniae 87001

Mycoplasma capricolum subsp. capripneumoniae (Mccp), belongs to Mycoplasma mycoides cluster and is a causal pathogen of contagious caprine pleuropneumonia (CCPP). This paper presents the complete annotated genome sequence of Mccp Strain 87001—a strain that was isolated from pneumonia affected goats on a farm in China, and comparative genomics analysis of five Mccp genomes in addition to comparative genomics within Mycoplasma mycoides cluster. The Mccp strain 87001 genome consists of a single circular chromosome 1017333 bp in length and encodes 898 open reading frames (orfs) averaging 944 bp in length. Fifty eight potential virulence genes were identified, including variable surface lipoproteins, hemolysin A, and P60 surface lipoprotein. Comparative genomic analysis revealed eight virulence genes and four extracellular genes which remained unchanged in five Mccp genomes for forty years, which can be used as potential target for drug development and vaccine design. We revealed 183 Mccp unique genes as markers to distinguish Mccp with other mycoplasma strains from goats, and different virulence factors contributing to host specificity and different syndrome of bovine pathogens and caprine pathogens.