Topic:Bayesian Analysis
Bayesian analysis is a statistical method that applies Bayes' theorem to update the probability of a hypothesis as more evidence or information becomes available. In equine research, Bayesian analysis can be used to interpret data and make probabilistic inferences about various aspects of horse health, behavior, and performance. This approach allows researchers to incorporate prior knowledge or expert opinion into the analysis, providing a flexible framework for dealing with complex datasets and uncertainty. Applications of Bayesian analysis in equine studies may include genetic evaluations, disease prevalence estimation, and performance prediction. This page compiles peer-reviewed research studies and scholarly articles that explore the application, methodology, and outcomes of Bayesian analysis in the context of equine science.
Seroprevalence of equine leptospirosis in Poland (2019-2023). Leptospirosis in horses is associated with various clinical signs, potentially leading to fatal outcomes. Additionally, the disease may pose a zoonotic risk to individuals involved in handling infected animals. Implementing a serological monitoring programme in the equine population is one of the key tools used to reduce the risk of transmission of Leptospira infections to humans. Objective: To provide new insights into the seroprevalence of leptospirosis in domestic horses in Poland. Methods: Serological monitoring program. Methods: Data were collected from serological surveys of horse serum ...
Unwelcome neighbours: Tracking the transmission of Streptococcus equi in the United Kingdom horse population. Strangles (Streptococcus equi infection) remains endemic in the UK, with ~300 laboratory diagnoses annually. Sub-clinically infected long-term carriers are considered a key driver of endemicity. Analysing genomes of circulating strains could provide valuable transmission insights of this pathogen. Objective: To determine the population structure and diversity of UK S. equi isolates and to model transmission using epidemiological and whole genome sequencing data. Methods: Retrospective cross-sectional epidemiological and genomic surveillance. Methods: A dated phylogenetic tree derived from 511...
The first mitogenome of Petrovinema skrjabini from Equus ferus przewalskii: a phylogenetic analysis within the Strongylidae family. Petrovinema skrjabini (Nematoda: Strongylidae, Cyathostominae) is a parasitic nematode colonizing the cecum and colon of equids. Like other cyathostomins, its larvae (L3) invade the intestinal mucosa, forming encysted nodules that may remain dormant for years. Mass larval emergence triggers larval cyathostominosis-a severe syndrome characterized by hemorrhagic typhlocolitis and diarrhea, with mortality rates exceeding 50%. However, owing to the morphological indistinguishability of cyathostomin and frequent mixed infections in natural settings, species-specific contributions to pathogenesis re...
An application of the MR-Horse method to reduce selection bias in genome-wide association studies of disease progression. Genome-wide association studies (GWAS) of disease progression are vulnerable to collider bias caused by selection of participants with disease at study entry. This bias introduces spurious associations between disease progression and genetic variants that are truly only associated with disease incidence. Methods of statistical adjustment to reduce this bias have been published, but rely on assumptions regarding the genetic correlation of disease incidence and disease progression which are likely to be violated in many human diseases. MR-Horse is a recently published Bayesian method to estimate...
A profiling of faecal parasites in horses in Mauritius and resistance to Fenbendazole at one horse-riding stable. Mauritius hosts a population of approximately 900 equids, but no investigations have delved into issues such as the prevalence of equine helminths, anthelmintic usage, and resistance emergence. This study aimed to devise a qualitative and quantitative profile of common helminthic intestinal parasites in equines at eight out of twenty-eight stables (272 horses, 29 % of local population) and to determine whether helminthic intestinal parasites in equines at one stable have developed resistance to Fenbendazole by quantitatively assessing pre-treatment faecal egg counts, post-treatment faecal egg...
Identification of Genetic Relationships and Group Structure Analysis of Yanqi Horses. The Yanqi horse is a distinguished local breed in China, known for its robust physique and strong adaptability. However, due to insufficient breeding populations and a loosely structured breeding system, the number of Yanqi horses has been declining annually. To protect its genetic resources and develop scientific breeding strategies, this study aimed to analyze the genetic diversity, parentage relationships, and genetic structure of the Yanqi horse conservation population using microsatellite markers. A total of 117 Yanqi horses were selected for genotyping analysis using 16 microsatellite ...
Bayesian Recursive and Structural Equation Models to Infer Causal Links Among Gait Visual Scores on Campolina Horses. Gait visual scores are widely applied to horse breeding because they are a fast and easy phenotyping strategy, allowing the numeric interpretation of a complex biological process such as gait quality. However, they may suffer from subjectivity or high environmental influence. We aimed to investigate potential causal relationships among six visual gait scores in Campolina horses. The data included 5475 horses with records for at least one of the following traits: Dissociation (Di), Comfort (C), Style (S), Regularity (R), Development (De), and Gait total Scores (GtS). The pedigree comprised thre...
Genetic diversity and phylogenetic relationships of Theileria equi inferred from heat shock protein 70 kDa gene sequences in Brazilian horses. Equine piroplasmosis, a tick-borne disease caused by hemoparasites of the Babesia and Theileria genera, has significant clinical and economic impacts worldwide. This study aims to characterize the heat shock protein 70 kDa (hsp70) gene sequences of Theileria equi from naturally infected horses across the five geographic regions in Brazil, and to analyze the phylogenetic relationships between T. equi and other parasites within the order Piroplasmida. Primers specific to T. equi were designed through in silico analysis of hsp70 gene sequences available in GenBank. Forty samples of equine whole ...
Influence of Sires on Population Substructure in Dülmen Wild Horses. The objectives of the present study were to analyze the influence of the stallions employed in the Dülmen wild horses on the genetic diversity and population substructure using Bayesian cluster analysis. The Dülmen wild horse is maintained as a unique horse population exposed to the natural conditions all year round in the Merfelder Bruch near Dülmen in Westphalia, Germany. Stallions selected for breeding have to prove their abilities to survive under this harsh environment. We used multilocus genotypic information from a set of 29 autosomal microsatellites to determine the paternity of 185...
Genetic Diversity and Population Structure of Dülmen Wild, Liebenthal and Polish Konik Horses in Comparison with Przewalski, Sorraia, German Draught and Riding Horses. The objective of the present study was to analyze the genetic diversity, individual-based assessment of population structure, and admixture in the Dülmen wild horse population in comparison to warmblood, coldblood, and primitive horse populations. The Dülmen wild horse is kept as a unique horse population in the Merfelder Bruch near Dülmen in Westphalia, Germany, and since 1856 has been managed by the Dukes of Croÿ. The Dülmen wild horse population is exposed to the natural conditions of the Merfelder Bruch all year round without human interventions for feeding and veterinary care. In the...
Methodological approaches to assessing the genetic predisposition of osteochondrosis of the tarsocrural joint in the Pura Raza Española horses. Osteochondrosis (OC) is a developmental orthopaedic disease of significant concern in numerous sport horse breeds, with significant international relevance. Using digital radiographs, we assessed the occurrence of hock (tarsocrural joint) OC in 3 048 Pura Raza Española (PRE) horses which took part in a morpho-functional test, in three specific locations in the tarsus limbs: the Distal Intermediate Ridge of the Tibia (DIRT), the lateral trochlear ridges of the talus (LTT), and the medial trochlear ridges of the talus (MTT). An incidence rate of 13.3% was found for hock OC in the analysed samp...
The first report of triple anthelmintic resistance on a French Thoroughbred stud farm. This study assessed the anthelmintic resistance in strongylid nematodes against commonly used anthelmintic (AH) drugs in a French galloping racehorse stud farm from March to December 2023. Faecal egg count reduction tests (FECRTs) were conducted in three different groups of Thoroughbred yearlings (a group of 6 males, a group of 13 females and a group of 8 females and 3 males) following the new World Association for the Advancement of Veterinary Parasitology (WAAVP) guidelines. The efficacy of fenbendazole was tested in two groups once during the monitoring period (in March), the efficacy of iv...
A national survey of anthelmintic resistance in ascarid and strongylid nematodes in Australian Thoroughbred horses. This study quantified the extent of anthelmintic resistance (AR) in ascarid and strongylid nematodes against commonly used anthelmintics in Australian Thoroughbred horses. Faecal egg count reduction tests (FECRTs, n = 86) and egg reappearance period (ERP) tests were conducted on 22 farms across Australia. Faecal egg counts (FECs) were determined using the modified McMaster technique, and percent faecal egg count reduction (%FECR) was calculated using the Bayesian hierarchical model and hybrid Frequentist/Bayesian analysis method. The results were interpreted using old (published in 1992) and...
Evaluation of field-testing protocols to diagnose insulin dysregulation in ponies using a Bayesian approach. Field tests and their association with laminitis have not been evaluated in large cohorts. The objectives of this study were to evaluate the performance of basal insulin (BI), the oral sugar test (OST) and the insulin tolerance test (ITT) to diagnose ID and investigate their association with laminitis. Insulin dysregulation status was determined in 146 ponies using BI (insulin concentration >20 µIU/mL), an OST (insulin concentration >65 µIU/mL at 60 or 90min after oral administration of 0.45mL/kg corn syrup) and an ITT (< 50% reduction in glucose concentration 30min after intravenous adminis...
Exposure levels of animal allergens, endotoxin, and β-(1,3)-glucan on a university campus of veterinary medicine. The study aimed to determine the allergen, endotoxin and β-(1,3)-glucan concentrations at various areas on a university campus of veterinary medicine. Methods: Dust samples were collected four times a year for three years using electrostatic dust collectors (EDC) at 25 different locations on a campus of veterinary medicine and in laboratories of inorganic chemistry as a control area representing animal-free environment. Major animal allergens from dog, cat, horse, cattle and mouse, domestic mite (DM) allergens, and β-(1,3)-glucan were measured using enzyme immunoassays and endotoxin using th...
Racing Performance of the Quarter Horse: Genetic Parameters, Trends and Correlation for Earnings, Best Time and Time Class. The aim of this study was to evaluate the sprint racing performance of Quarter Horses in Brazil. Estimating genetic parameters, trends and correlations were obtained by single- and two-trait analyses using Bayesian inference (earnings to 2 years of equestrian age, best time and time class at distances of 301 m and 402 m). The data comprised a period of 38 equestrian years (1978 to 2015) with 23,482 sprint race records from 5861 animals. The heritability estimates were of low to moderate magnitude, ranging from 0.10 to 0.37 (single-trait) and from 0.15 to 0.41 (two-traits), and the repeatabilit...
The Relevance of the Expected Value of the Proportion of Arabian Genes in Genetic Evaluations for Eventing Competitions. The Arabian horse is a generally reliable sport horse, and continues to be a remarkable endurance horse, so the relevance of the expected value of the proportion of Arabian genes (EV%AG) in horses participating in eventing could be a relevant factor. A total of 1089 horses participating in eventing (8866 records) were used. A GLM revealed that the EV%AG was significant in dressage, show jumping and cross-country. A BLUP genetic evaluation was computed with five genetic models (without the EV%AG (0) using as a covariate (A), as a fixed effect (B), with variance heterogeneity, and in genetic gro...
Prevalence and genetic diversity of Theileria equi from horses in Xinjiang Uygur Autonomous region, China. Theileria equi is a tick-borne intracellular apicomplexan protozoan parasite that causes equine theileriosis (ET). ET is an economically important disease with a worldwide distribution that significantly impacts international horse movement. Horses are an essential part of the economy in Xinjiang which is home to ∼10% of all the horses in China. However, there is very limited information on the prevalence and genetic complexity of T. equi in this region. Blood samples from 302 horses were collected from May to September 2021 in Ili, Xinjiang, and subjected to PCR examination for the presence...
Estimating Temporally Variable Selection Intensity from Ancient DNA Data. Novel technologies for recovering DNA information from archaeological and historical specimens have made available an ever-increasing amount of temporally spaced genetic samples from natural populations. These genetic time series permit the direct assessment of patterns of temporal changes in allele frequencies and hold the promise of improving power for the inference of selection. Increased time resolution can further facilitate testing hypotheses regarding the drivers of past selection events such as the incidence of plant and animal domestication. However, studying past selection processes ...
Molecular Features and Antimicrobial Susceptibilities of Streptococcus equi ssp. equi Isolates from Strangles Cases in Indonesia. Strangles, caused by ssp. (), is a highly infectious and frequent disease of equines worldwide. No data are available regarding the molecular epidemiology of strangles in Indonesia. This study aimed to characterize isolates obtained from suspected strangles cases in Indonesia in 2018. Isolates originated from seven diseased horses on four different farms located in three provinces of Indonesia. Whole genome sequences of these isolates were determined and used for typing, multilocus sequence typing (MLST), and core genome MLS typing (cgMLST). Genomes were also screened for known antimicrobi...
Bayesian accuracy estimates and fit for purpose thresholds of cytology and culture of endometrial swab samples for detecting endometritis in mares. The overall aim of this work was to identify the potential impact of misclassification errors associated with routine screening and diagnostic testing for endometritis in mares. Using Bayesian latent class models (BLCM), specific objectives were to: 1) estimate the diagnostic accuracy of cytology and culture of endometrial swab samples to detect endometritis in mares; 2) assess the impact of different cytology thresholds on test accuracy and misclassification costs; and 3) assess the sensitivity (Se) and specificity (Sp) of a diagnostic strategy including both tests interpreted in series and p...
Anthelmintic resistance of horse strongyle nematodes to fenbendazole in Lithuania. Control of strongyle infections presents a global challenge for horse practitioners due to the development of anthelmintic resistance (AR), however comprehensive information on AR in Lithuania is still lacking. The aim of this study was to assess the current situation of fenbendazole (FBZ) AR in horses at stable level in Lithuania. Results: Faecal samples from 121 horses from six stables were examined using the Mini-FLOTAC method. Of these, 89 horses met the inclusion criteria that included strongyle faecal egg counts (FEC) exceeding 200 eggs per gram (EPG). Faecal egg count reduction tests (F...
Morpho-Functional Traits in Pura Raza Menorquina Horses: Genetic Parameters and Relationship with Coat Color Variables. The studbook of Pura Raza Menorquina horses only permits the use of black-coated animals with a small quantity of white marks as breeding stock. Its breeding program uses linear morpho-functional traits as selection criteria. Our aim was to estimate the genetic parameters of linear morpho-functional traits, and reveal relationship of quality of black coat color (QB) and percentage of white marks (WM) with the other morphological and functional linear traits in this breed. A total of 46 linear traits were scored by four appraisers using seven classes, with a total of 772 records from 333 animal...
Occurrence of Equine Foamy Virus Infection in Horses from Poland. Equine foamy virus (EFVeca) is a foamy virus of non-primate origin and among the least-studied members of this retroviral subfamily. By sequence comparison, EFVeca shows the highest similarity to bovine foamy virus. In contrast to simian, bovine or feline foamy viruses, knowledge about the epidemiology of EFVeca is still limited. Since preliminary studies suggested EFVeca infections among horses in Poland, we aimed to expand the diagnostics of EFVeca infections by developing specific diagnostic tools and apply them to investigate its prevalence. An ELISA test based on recombinant EFVeca Gag pr...
Population structure and genomic footprints of selection in five major Iranian horse breeds. The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, thre...
Phylogenetic and Mutation Analysis of the Venezuelan Equine Encephalitis Virus Sequence Isolated in Costa Rica from a Mare with Encephalitis. Venezuelan Equine Encephalitis virus (VEEV) is an arboviral pathogen in tropical America that causes lethal encephalitis in horses and humans. VEEV is classified into six subtypes (I to VI). Subtype I viruses are divided into epizootic (IAB and IC) and endemic strains (ID and IE) that can produce outbreaks or sporadic diseases, respectively. The objective of this study was to reconstruct the phylogeny and the molecular clock of sequences of VEEV subtype I complex and identify mutations within sequences belonging to epizootic or enzootic subtypes focusing on a sequence isolated from a mare in C...
Evaluation of factors associated with surgical site infection in equine proximal interphalangeal joint arthrodesis: 54 cases (2010-2019). The frequency of surgical site infection (SSI) following orthopaedic implant placement in horses has been reported but not compared with respect to specific antibiotic protocols administered. To determine factors associated with SSI in horses undergoing proximal interphalangeal joint (PIPJ) arthrodesis including perioperative antibiotic protocols. Records were evaluated (2010-2019), and horses undergoing PIPJ arthrodesis were identified. Patient signalment, supervising surgeon, reason for surgery, limb, implants placed, anaesthetic time, duration casting/coaptation postoperatively, antibiotic ...
How far away do you keep your equines? Estimation of the equine population’s spatial distribution in France. It is essential to have an accurate picture of the spatial distribution of equines to be able to monitor equine health events effectively. In France, this information is only available for certain categories of live equines kept in professional structures and for dead equines removed by renderers. This limits the surveillance, prevention and control methods able to be used to prevent the spread of equine diseases. Our study aimed to provide a realistic estimate of the spatial distribution of the French equine population at the detailed scale of the French commune (France's smallest administrat...
Investigation of cross-regional spread and evolution of equine influenza H3N8 at US and global scales using Bayesian phylogeography based on balanced subsampling. Equine influenza virus (EIV) is a highly contagious pathogen of equids, and a well-known burden in global equine health. EIV H3N8 variants seasonally emerged and resulted in EIV outbreaks in the United States and worldwide. The present study evaluated the pattern of cross-regional EIV H3N8 spread and evolutionary characteristics at US and global scales using Bayesian phylogeography with balanced subsampling based on regional horse population size. A total of 297 haemagglutinin (HA) sequences of global EIV H3N8 were collected from 1963 to 2019 and subsampled to global subset (n = 67), raw US ...
Reduced rank analysis of morphometric and functional traits in Campolina horses. Multitrait models can increase the accuracy of breeding value prediction and reduce bias due to selection by using traits measured before and after it has occurred. However, as the number of traits grows, a similar trend is expected for the number of parameters to be estimated, which directly affects the computing power and the amount of data required. The aim of the present study was to apply reduced rank (principal components model-PCM) and factor analytical models (FAM), to estimate (co)variance components for nineteen traits, jointly evaluated in a single analysis in Campolina horses. A to...