Phylogeographic and population genetic structure of hound-like native dogs of the Mediterranean Basin.

The dog was probably the first domesticated animal. Despite extensive archaeological and genetic investigations, the origin and the evolution of the extant dogs are still being debated. Dog breeds that have over time been selected for hunting share common ancestral traits. This study represents the first comprehensive attempt to survey at the genomic and mitochondrial level eight hound-like dogs breeds indigenous to the Mediterranean Basin to determine if they share common ancient origins. Results from the microsatellite analysis indicate that all the dog populations have a low inbreeding value.The Kelb tal-Fenek has a high divergence from the current Egyptian street population, however there is not enough evidence from this study to exclude completely the potential of an ancient common relationship. Overall, the mitochondrial results indicate high frequencies of haplogroups A and B and a low representation of haplogroup C, while only one Egyptian dog could be assigned to haplogroup D. Results reveal identities and shared clades, suggesting the conservation of ancient European mitotypes in the Mediterranean hound-like breeds, especially in the Egyptian population. Although none of the dog populations/breeds participating in this study indicate to be direct descendants of the Egyptian dogs, they still have a very close morphologically resemblance to those iconic Egyptian dogs often depicted in ancient art forms and share some genetic links with the current Egyptian population. Further research is required with other markers such us complete mitogenomes and SNP panels to confirm the complex history of the Mediterranean dogs involved in this study.

Coxiella burnetii and Co-Infections with Other Major Pathogens Causing Abortion in Small Ruminant Flocks in the Iberian Peninsula.

Coxiella burnetii is an intracellular bacterium causing human Q fever and reproductive disorders in domestic ruminants. We analyzed the occurrence of C. burnetii and co-infections with six other major pathogens causing abortion in sheep (1242 cases) and goat (371 cases) flocks from Spain and Portugal. After real-time PCR detection, co-infections were established by principal component and cluster analysis that grouped cases based on the joint presence/absence of several microorganisms. C. burnetii and Chlamydia abortus were the most common abortifacient agents with approximately 75% of cases from both hosts testing positive, followed by Toxoplasma gondii, Campylobacter sp., Salmonella enterica, border disease virus and Neospora caninum. C. burnetii was significantly more common than C. abortus in goat abortions (p < 0.001). Co-infections with at least two pathogens were found in more than 66% cases of ovine abortions and 36% cases of caprine abortions testing positive for C. burnetii, mostly including mixed infections with only C. abortus. These findings indicate that both pathogens are the most significant ones to be readily prevented by vaccination in this geographical area. Biosecurity and biocontainment measures are also steadfastly recommended to prevent both the economic losses and public health risks associated with most of these abortifacient agents.

Occurrence of Rotavirus A Genotypes and Other Enteric Pathogens in Diarrheic Suckling Piglets from Spanish Swine Farms.

Species A rotavirus (RVA) is a major viral pathogen causing diarrhea in suckling piglets. Studies on its genetic heterogeneity have implications for vaccine efficacy in the field. In this study, fecal samples (n = 866) from diarrheic piglets younger than 28 days were analyzed over a two-year period (2018-2019). Samples were submitted from 426 farms located in 36 provinces throughout Spain and were tested using real-time PCR (qPCR) and reverse transcription real-time PCR (RT-qPCR) for five enteric pathogens. The individual prevalence was 89.4%, 64.4%, 44.9%, 33.7% and 4.4% for Clostridiumperfringens, Clostridioides (formerly Clostridium) difficile, species A rotavirus, species C rotavirus and porcine epidemic diarrhea virus, respectively. Most specimens (96.9%) were positive for at least one of the target pathogens, and more than 80% of samples harbored mixed infections. Nucleotide sequencing of 70 specimens positive for RVA revealed the presence of the VP7 genotypes G4, G9, G3, G5, G11 and the VP4 genotypes P7, P23, P6 and P13, with the combinations G4P7 and G9P23 being the most prevalent, and especially in the areas with the highest pig population. The study shows the extensive genetic diversity of RVA strains as well as discrepancies with the genotypes contained in the vaccine available in Spain, and multiple amino acid differences in antigenic epitopes of different G- and P- genotypes with the vaccine strains. Further investigations are needed to determine the efficacy of the vaccine to confer clinical protection against heterologous strains.

Periodontal and Dental Status in Packs of Spanish Dogs.

While periodontal disease (PD) is the most common canine oral pathology, its prevalence varies according to diagnosis methodology, breed, and age. We intended to increase understanding of canine PD by studying dogs that are managed in a specific way: pack dogs in Spain. They received a mixed diet (home-prepared food, commercial dry food, stale bread and bones). Thirty-two conscious individuals from two packs of dogs in Northeastern Spain (30/32 crossbred hunting dogs and 2/32 Siberian Husky; 26 males and 6 females; 27.75 ± 5.807 kgs; 5.48 ± 2.818 years) received visual dental examination for assessment of absent teeth (AT), dental calculus (DC) grade, gingival recession (GR), periodontal disease (PD), tooth fracture (TF), and dental attrition (DA). DC was the most prevalent oral problem (75%), followed by TF/DA (68.75%), AT (34.37%), GR (31.25%), and, finally, PD (15.62%). Low individual affectation values were found for AT, GR, and PD (<1 tooth/individual); mean DC grade per individual was 0.06 ± 0.063; and TF and DA were found in 1.63 and 4.72 teeth/individual, respectively. Low prevalence and extent of PD was attributed to diagnosis methodology, bodyweight effect, breed, and, ultimately, diet. Individuals affected by DC remained under veterinary surveillance due to PD development.

Occurrence and genetic diversity of rotavirus A in faeces of diarrheic calves submitted to a veterinary laboratory in Spain.

A total of 237 faecal specimens from diarrheic calves younger than two months were collected and submitted for diagnosis of enteropathogens over a two-year period (2017-2018) to a veterinary laboratory. Samples originated from 193 dairy and beef farms in 29 provinces distributed throughout Spain, and were tested for the occurrence of three target enteric pathogens by reverse transcription real-time PCR (RT-qPCR): bovine rotavirus A (RVA), Cryptosporidium parvum and bovine coronavirus (BCoV). RT-PCR and nucleotide sequencing analysis were used to determine the G (VP7 gene) and P (VP4 gene) genotypes of 26 specimens positive for RVA. A total of 188 specimens (79.3 %) were positive for at least one of the three target enteric pathogens, and 101 samples (42.6 %) harbored mixed infections. The individual prevalence was 57.8 %, 50.6 % and 23.6 % for C. parvum, RVA and BCoV, respectively. Molecular analysis of selected RVA strains revealed the presence of the G6, G10, G3, P[5] and P[11] genotypes, with the combinations G6P[5] and G6P[11] being the most prevalent. Alignments of nucleotide sequences of the VP7 and VP4 markers showed a high frequency of single nucleotide polymorphisms (SNPs), with up to 294 SNPs found in 869bp of sequence at the G6 genotype (0.338 SNPs/nt), which reveals the extensive genetic diversity of RVA strains. Phylogenetic analysis of the VP7 gene of the G6 strains revealed four distinct lineages, with most strains clustering in the G6-IV lineage. The discrepancies between the RVA genotypes circulating in the sampled cattle farms and the genotypes contained in commercial vaccines currently available in Spain are discussed. We believe that this is the first study on the molecular characterization of rotavirus infecting cattle in Spain.

Multilocus fragment analysis of Cryptosporidium parvum from pre-weaned calves in Colombia.

The intra-species genetic diversity of Cryptosporidium parvum in dairy cattle farms in the central area of Colombia was investigated using a multilocus fragment typing approach with nine variable-number tandem-repeat (VNTR) loci and the gp60 gene. Genomic DNA of 70 C. parvum isolates from pre-weaned calves in 32 farms was analysed. Most markers showed two (ML1, MSB, CP47, and MSC6-7) or three alleles (5B12, Cgd2_3850, and Cgd6_5400), although they exhibited a major allele accounting for more than 69% of specimens, which explains their low discriminatory index. The TP14 microsatellite was monomorphic while a total of six alleles were found at the ML2 microsatellite. The two novel allelic variants (219bp, 245bp) exhibited by more than 36% of specimens at the latter locus were a remarkable finding. The 10-markers typing tool provided a Hunter-Gaston discriminatory value of 0.940 (95% CI, 0.918 - 0.961) and differentiated 22 multilocus subtypes (MLTs). Nevertheless, the combination of the three most informative markers (ML2, gp60, and Cgd2_3850) differentiated 68% of MLTs and hardly impaired the discriminatory index. The fact that many MLTs (13/22) were distinctive for individual farms provides evidence for the endemic nature of the infection and the major role played by transmission within farms. The eBURST algorithm suggested a low degree of genetic divergence. All but three MLTs were clustered in a clonal complex with a star-like topology typical of clonal expansion, however linkage analysis did not find evidence of linkage disequilibrium. Bayesian analysis also identified a genetic structure with K = 3 being the best estimation of ancestral clusters, although a large proportion of isolates (35%) could not be allocated to a single population, which indicates their mixed origin. The results confirm the genetic distinctiveness of C. parvum in cattle farms in this geographical area. This is the first multilocus analysis on the intra-specific variability of Cryptosporidium from calves in South America.

Influence of Sex and Age on Posterior Semicircular Canal Thickness.

OBJECTIVE: The aim of this study is to determine whether sex and age influence posterior semicircular canal (PSC) thickness. METHODS: This observational study was conducted in 3 tertiary hospitals. The minimal distance between the PSC and the posterior cranial fossa (PSC thickness) was estimated by thin-section multidetector row computed axial tomography (CAT) scan of the temporal bones. Nonselected consecutive patients of all ages (607 temporal bones) were considered. RESULTS: A significant effect was only detected for sex (F = 5.418, p = 0.020); PSC thickness showed a higher mean value in women (mean difference ± SE: 0.224 ± 0.096 mm). A significant and negative r value was detected for males aged >45 years (-0.173, p = 0.026); in that group of patients, PSC thickness decreased as age increased (0.018 ± 0.008 mm/year). For females aged ≤45 years, a significant and positive r value was found (0.198, p = 0.022); in that group, PSC thickness increased as age increased (0.020 ± 0.008 mm/year). CONCLUSIONS: PSC thickness did not significantly evolve with age in young males (≤45 years) but it decreased from age 45 years onwards. On the other hand, PCS thickness increased with age in women until the age of 45 years and it did not significantly change in older females.

Intra-Species Genetic Diversity and Clonal Structure of Cryptosporidium parvum in Sheep Farms in a Confined Geographical Area in Northeastern Spain.

A multilocus fragment typing approach including eleven variable-number tandem-repeat (VNTR) loci and the GP60 gene was used to investigate the intra-farm and intra-host genetic diversity of Cryptosporidium parvum in sheep farms in a confined area in northeastern Spain. Genomic DNA samples of 113 C. parvum isolates from diarrheic pre-weaned lambs collected in 49 meat-type sheep farms were analyzed. Loci exhibited various degrees of polymorphism, the finding of 7-9 alleles in the four most variable and discriminatory markers (ML2, Cgd6_5400, Cgd6_3940, and GP60) being remarkable. The combination of alleles at the twelve loci identified a total of 74 multilocus subtypes (MLTs) and provided a Hunter-Gaston discriminatory index of 0.988 (95% CI, 0.979-0.996). The finding that most MLTs (n = 64) were unique to individual farms evidenced that cryptosporidial infection is mainly transmitted within sheep flocks, with herd-to-herd transmission playing a secondary role. Limited intra- host variability was found, since only five isolates were genotypically mixed. In contrast, a significant intra-farm genetic diversity was seen, with the presence of multiple MLTs on more than a half of the farms (28/46), suggesting frequent mutations or genetic exchange through recombination. Comparison with a previous study in calves in northern Spain using the same 12-loci typing approach showed differences in the identity of major alleles at most loci, with a single MLT being shared between lambs and calves. Analysis of evolutionary descent by the algorithm eBURST indicated a high degree of genetic divergence, with over 41% MLTs appearing as singletons along with a high number of clonal complexes, most of them linking only two MLTs. Bayesian Structure analysis and F statistics also revealed the genetic remoteness of most C. parvum isolates and no ancestral population size was chosen. Linkage analysis evidenced a prevalent pattern of clonality within the parasite population.

Bilateral Ovotestes in a 78, XX SRY-Negative Beagle Dog.

This report describes a disorder of the sexual development in a beagle dog resulting in an intersex condition. A 6 mo old beagle was presented for evaluation of a protruding structure from the vulva consistent with an enlarged clitoris. Ultrasonographic examination revealed the presence of both gonadal and uterine structures. Retrograde cystourethrovaginogram showed the presence of an os clitoris and severe vaginal stenosis. Histological studies revealed the presence of bilateral ovotestes and uterus. The gonad had interstitial cells within seminiferous-like tubules lined only with Sertoli cells and abundant interstitial cells among primordial, primary, and secondary follicles. Hormone assays completed before and after gonadohysterectomy showed an elevation in the levels of progesterone and dihydrotestosterone that returned to baseline 3 mo after surgery. Testosterone levels that were within the male reference ranges before surgery decreased to basal levels postsurgically. 17-ß-Estradiol levels showed little variation and values were always within the reference ranges for a male. Cytogenetic analysis showed a normal female karyotype (2n = 78, XX) and polymerase chain reaction analysis revealed the absence of the sex-determining region Y gene. In summary, the dog presented bilateral ovotestes and a 2n = 78, XX chromosomal complement lacking the sex determining region Y gene, consistent with a diagnosis of true hermaphroditism.

In silico identification and three-dimensional modelling of the missense mutation in ADAMTS2 in a sheep flock with dermatosparaxis.

BACKGROUND: Dermatosparaxis (Ehlers-Danlos syndrome in humans) is characterized by extreme fragility of the skin. It is due to the lack of mature collagen caused by a failure in the enzymatic processing of procollagen I. We investigated the condition in a commercial sheep flock. HYPOTHESIS/OBJECTIVES: Mutations in the ADAM metallopeptidase with thrombospondin type 1 motif, 2 (ADAMTS2) locus, are involved in the development of dermatosparaxis in humans, cattle and the dorper sheep breed; consequently, this locus was investigated in the flock. ANIMALS: A single affected lamb, its dam, the dam of a second affected lamb and the rams in the flock were studied. METHODS: DNA was purified from blood, PCR primers were used to detect parts of the ADAMS2 gene and nucleotide sequencing was performed using Sanger's procedure. Skin samples were examined using standard histology procedures. RESULTS: A missense mutation was identified in the catalytic domain of ADAMTS2. The mutation is predicted to cause the substitution in the mature ADAMTS2 of a valine molecule by a methionine molecule (V15M) affecting the catalytic domain of the enzyme. Both the 'sorting intolerant from tolerant' (SIFT) and the PolyPhen-2 methodologies predicted a damaging effect for the mutation. Three-dimensional modelling suggested that this mutation may alter the stability of the protein folding or distort the structure, causing the protein to malfunction. CONCLUSIONS AND CLINICAL IMPORTANCE: Detection of the mutation responsible for the pathology allowed us to remove the heterozygote ram, thus preventing additional cases in the flock.

New contributions to the study of common double mutants in the human LDL receptor gene.

Variations in the gene encoding the low-density lipoprotein receptor (LDLR) can cause familial hypercholesterolemia (FH), one of the most common inherited metabolic disorders in humans. The functional effects of the p.Gln92Glu and p.Asn564His alterations are predicted as benign, but the c.313 + 1G>C and p.Lys799_Phe801del changes are believed to cause disease. Although p.Gln92Glu and c.313 + 1G>C have been observed only in Spain, p.Asn564His and p.Lys799_Phe801del are widespread in Western Europe. In order to estimate the ages (t generations) of these four variants of the gene, to determine their possible origin and to consider the influence of age and selective pressure on their spread, we analyzed 86 healthy individuals and 126 FH patients in Spain. Most of the FH patients investigated carried two of these four LDLR variants simultaneously, while only one patient carried three of them simultaneously. Haplotype analyses were based on five LDLR SNPs: c.81T>C, c.1413G>A, c.1725C>T, c.1959T>C and c.2232G>A. The results suggest that p.Gln92Glu and c.313 + 1G>C arose at about the same time (99 and 103 generations ago, respectively) in the CACTG haplotype and that p.Asn564His and p.Lys799_Phe801del appeared in the CGCCG haplotype and might be slightly more recent variations (92 and 95 generations ago, respectively). Low selective pressures could explain the maintenance of these variants in spite of their ages. The origin of p.Gln92Glu and c.313 + 1G>C appears to be in Spain whereas p.Asn564His and p.Lys799_Phe801del could have been introduced in Spain by Celtic migrations in the seventh to fifth centuries BC.

Mitochondrial DNA diversity in Francolinus pondicerianus interpositus (grey francolin, Galliformes) from Pakistan.

Francolinus pondicerianus interpositus (grey francolin, Galliformes) is the only francolin present in the Suleiman Range (central Pakistan), one of the poorest and least developed areas in Pakistan. As a game bird, the francolin is an important income source for the region, but no demographic data are available. Therefore, the aim of this work was to study the polymorphism pattern of the Control Region gene (mitochondrial DNA, mtDNA), in order to obtain some initial information about genetic diversity, possible structure and demographic dynamics in this population. In 29 individuals captured in four sampling areas in the western and the eastern Suleiman Range, we detected nine polymorphic sites in a 511 bp fragment of the mtDNA Control Region gene, resulting in seven haplotypes. Haplotype (h = 0.818 ± 0.032) and nucleotide diversity (π % = 0.308 ± 0.210) values suggested a large population size and a low divergence among the haplotypes. AMOVA (Φ(ST) = 0.005; P = 0.352) did not detect any significant differences among the western and eastern populations; therefore, specimens of both sampled areas could be considered as drawn from a single population. The observed distribution of pairwise mismatches was bimodal, revealing significant departure from a growing-decreasing population model (P = 0.030); these results would point to a demographic equilibrium. Tribal control of hunting might provide an explanation for this situation, but future overhunting would threaten the survival of this population.

Malformations of the epididymis, incomplete regression of the mesonephric tubules and hyperplasia of Leydig cells in canine persistence of Müllerian duct syndrome.

Persistence of the Müllerian duct syndrome (PMDS) is a rare form of pseudohermaphroditism characterized by the presence of uterus and oviducts in otherwise normally differentiated SRY-positive 78 XY canine males. Undescended testicles are also common. We report a case of a male PMDS dog with a uterus and bilateral cryptorchidism. The dog had an incomplete regression of the mesonephric tubules. As a consequence of this an abnormally enlarged head of the epididymis was observed. In addition, an extreme reduction in size of both the body and the tail was found. Microscopic examination of both testicles revealed bilateral hyperplasia of Leydig cells. The progesterone blood level was measured by ELISA and was found to be abnormally high (3.18 ng/ml) compared to that of normal male dogs (lower than 1 ng/ml). Three months after surgical removal of the internal genitalia, the serum progesterone, testosterone and oestradiol levels were normal for a castrated male dog.

A 17 bp deletion in the Bone Morphogenetic Protein 15 (BMP15) gene is associated to increased prolificacy in the Rasa Aragonesa sheep breed.

Different mutations in the Bone Morphogenetic Protein 15 (BMP15) and the Growth Differentiation Factor 9 (GDF9) genes cause increased ovulation rate and infertility in a dosage-sensitive manner in sheep. They cause increased ovulation rate and twin and triplet births in heterozygotes, and complete primary ovarian failure in homozygotes resulting in total infertility. We are here presenting a novel mutation in the second exon of the ovine BMP15 gene, found in the Spanish breed Rasa Aragonesa. It consists of a 17 bp deletion resulting in displacement of the open reading frame and premature stop codons. As a consequence, nearly 85% of the sequence of the wild type aminoacidic chain in the second exon of the BMP15 pro-protein is modified or suppressed as only the first 45 amino acids are conserved of the 245 original. The mature peptide is lost. The ewes heterozygous for this deletion present very high prolificacy (2.66 lambs/birth) when compared to a mean flock prolificacy of 1.36 lambs. The deletion causes a complete lack of functionality of the second exon of BMP15, comparable to the effect of premature stop codons in other mutations. Therefore, homozygous females for the deletion are expected to present primary ovarian failure. DNA sequence analysis of the GDF9 coding regions detected only a synonymous Single Nucleotide Polymorphism (SNP), apparently not linked to changes in prolificacy.

Introgression of Alectoris chukar genes into a Spanish wild Alectoris rufa population.

In order to detect introgression of other Alectoris genus species into wild populations of Spanish Alectoris rufa, we studied a sample of 93 red-legged partridges (supposed to be A. rufa) captured in the island of Majorca. A set of 31 chukar partridges (Alectoris chukar) from Cyprus and 33 red-legged partridges (A. rufa) from one Spanish farm were also studied to provide suitable populations for comparison. Factorial correspondence analysis on microsatellite genotypes supported a clear distinction of birds from Cyprus, whereas partridges from Majorca and the Spanish farm overlapped in a wide area. The existence of A. chukar mitochondrial DNA in 16 individuals from Majorca indicated introgression into their maternal lineage even if their phenotypes were not different from A. rufa. Bayesian inference based on microsatellite analysis indicated a noticeable degree of genetic proximity to A. chukar only for one of these hybrids.

Mapping and characterization of the dominant black colour locus in sheep.

Dominant black pigment synthesis in sheep is caused by alterations of the melanocortin-1 receptor (MC1-R) coding sequence. Using five bovine microsatellite markers we have mapped the sheep MC1-R gene to chromosome 14, corresponding to the location in other mammalian species. The existence of two independent mutations, both causing an amino acid substitution, in distantly related breeds of sheep, support the hypothesis that the observed black pigment synthesis is caused by a mutual effect of the two mutations. As similar mutations are found separately at both locations in dominant black variants of other animal species, it is also possible that any of the two mutations could be sufficient for a partial pigment switch.