An Epigenetic Aging Clock for Cattle Using Portable Sequencing Technology

Extensively grazed cattle are often mustered only once a year. Therefore, birthdates are typically unknown or inaccurate. Birthdates would be useful for deriving important traits (growth rate; calving interval), breed registrations, and making management decisions. Epigenetic clocks use methylation of DNA to predict an individual’s age. An epigenetic clock for cattle could provide a solution to the challenges of industry birthdate recording. Here we derived the first epigenetic clock for tropically adapted cattle using portable sequencing devices from tail hair, a tissue which is widely used in industry for genotyping. Cattle (n = 66) with ages ranging from 0.35 to 15.7 years were sequenced using Oxford Nanopore Technologies MinION and methylation was called at CpG sites across the genome. Sites were then filtered and used to calculate a covariance relationship matrix based on methylation state. Best linear unbiased prediction was used with 10-fold cross validation to predict age. A second methylation relationship matrix was also calculated that contained sites associated with genes used in the dog and human epigenetic clocks. The correlation between predicted age and actual age was 0.71 for all sites and 0.60 for dog and human gene epigenetic clock sites. The mean absolute deviation was 1.4 years for animals aged less than 3 years of age, and 1.5 years for animals aged 3–10 years. This is the first reported epigenetic clock using industry relevant samples in cattle.

Mitochondrial Sequence Variation, Haplotype Diversity, and Relationships Among Dromedary Camel-Types

Dromedary camels are outstanding livestock that developed efficient abilities to tolerate desert conditions. Many dromedary camel-types (i.e., named populations) exist but lack defined specific breed standards, registries, and breeders’ governing organizations. The breed status of dromedary camel-types can partly be assessed by exploring mitochondrial DNA (mtDNA) variation. Accordingly, this study aimed to examine the breed status and the inter-population relationships of dromedary camel-types by analyzing sequence variation in the mtDNA control region and in three coding genes [cytochrome b, threonine, and proline tRNA, and part of the displacement loop (D-loop)] (867 bp region). Tail hair samples (n = 119) that represent six camel-types from Kuwait were collected, extracted, sequenced, and compared to other publicly available sequences (n = 853). Within the sequenced mitochondrial region, 48 polymorphic sites were identified that contributed to 82 unique haplotypes across 37 camel-types. Haplotype names and identities were updated to avoid previous discrepancies. When all sequences were combined (n = 972), a nucleotide diversity of 0.0026 and a haplotype diversity of 0.725 was observed across the dromedary-types. Two major haplogroups (A and B) were identified and the B1 haplotype was predominant and found in almost all dromedary-types whereas the A haplotypes were more abundant in African regions. Non-metric multidimensional scaling revealed an increased similarity among Arabian Peninsula “Mezayen” camel-types, despite their defining coat colors. The relationships among dromedary camel-types can partly be explained by mtDNA. Future work aimed at a deeper understanding of camel-type breed status should focus on a high number of nuclear markers.

Development of a morphological key for the southern salt marsh harvest mouse using genetically verified individuals

The salt marsh harvest mouse (SMHM; Reithrodontomys raviventris) is a state and federally listed endangered species endemic to the coastal marshes of the San Francisco Estuary of California. Of two subspecies, the southern (R. r. raviventris) is most endangered and lacks reliable morphological field tools to distinguish from the sympatric western harvest mouse (WHM; R. megalotis). We trapped and collected genetic samples and morphological data from 204 harvest mice from 14 locations from across the range of the southern SMHM. Genetic species identification indicated these to be composed of 48 SMHM and 156 WHM, which we compared at ten morphological characters. Most continuous characters overlapped between species. Color characters were significantly differentiated and we identified a number of species-specific diagnostic pelage categories in both species. A random forest analysis indicated that ventral coloration of the abdomen and the ventral tail hair color were the most useful for differentiating between species. We used these two morphological characters to develop a decision tree which correctly classified 94% of harvest mice to species with 99% accuracy. These findings suggest that our decision tree can be used to reliably identify the species of most harvest mice in the range of the southern SMHM, with a small proportion (6% in our study) needing genetic confirmation. The decision tree should be tested on additional harvest mice that were not used in its development, particularly from novel locations across the range.

The tail-tale of stress: an exploratory analysis of cortisol levels in the tail-hair of captive Asian elephants

Background Assessment of physiological states by measuring biomarkers, such as cortisol, has significantly contributed to the monitoring of health, welfare and management of animals. Immunoreactive cortisol in hair (hC) has been used widely for deciphering ‘stressful’ past-events in various wild and captive animals. However, no such studies have been done in long-lived mammals. Methods In this first exploratory study in elephants, we assessed (i) tail-hair growth rate (TGR) and (ii) hC levels in tail-hair samples from six captive Asian elephants from two zoos in Japan for comparing hC levels with zoo-keepers’ records of distinct biological events over a c.0.5–2.0-year period. Tail-hair samples were cut into segments (based on monthly growth rate), pulverized or minced and a validated cortisol enzyme-immunoassay employed to measure hC levels. Results When the hC levels of all individuals were compared with the keepers’ records, a posteriori, most of the high hC levels were found to be associated with ‘stressful’ or distinct behavioural events such as pathological (anaemia, colic infection, skin infection, oral sores), psychosocial (reluctance in entering the enclosure, presence of a calf) and husbandry practice-related (contact trials/ space sharing) conditions, indicating that tail-hair indeed can be a potential ‘retrospective’ calendar of physiological health of an animal. Conclusions Our observations open up the possibility of using the tail-hair as an alternative matrix to reconstruct the physiological history of elephants.

Tracking animal movements using biomarkers in tail hairs: a novel approach for animal geolocating from sulfur isoscapes

Background Current animal tracking studies are most often based on the application of external geolocators such as GPS and radio transmitters. While these technologies provide detailed movement data, they are costly to acquire and maintain, which often restricts sample sizes. Furthermore, deploying external geolocators requires physically capturing and recapturing of animals, which poses an additional welfare concern. Natural biomarkers provide an alternative, non-invasive approach for addressing a range of geolocation questions and can, because of relatively low cost, be collected from many individuals thereby broadening the scope for population-wide inference. Methods We developed a low-cost, minimally invasive method for distinguishing between local versus non-local movements of cattle using sulfur isotope ratios (δ34S) in cattle tail hair collected in the Greater Serengeti Ecosystem, Tanzania. Results We used a Generalized Additive Model to generate a predicted δ34S isoscape across the study area. This isoscape was constructed using spatial smoothers and underpinned by the positive relationship between δ34S values and lithology. We then established a strong relationship between δ34S from recent sections of cattle tail hair and the δ34S from grasses sampled in the immediate vicinity of an individual’s location, suggesting δ34S in the hair reflects the δ34S in the environment. By combining uncertainty in estimation of the isoscape, with predictions of tail hair δ34S given an animal’s position in the isoscape we estimated the anisotropic distribution of travel distances across the Serengeti ecosystem sufficient to detect movement using sulfur stable isotopes. Conclusions While the focus of our study was on cattle, this approach can be modified to understand movements in other mobile organisms where the sulfur isoscape is sufficiently heterogeneous relative to the spatial scale of animal movements and where tracking with traditional methods is difficult.

Prevalência de oxiuríase em equinos do Centro Hípico do 3º Regimento de Cavalaria de Guarda do Exército Brasileiro*

The objective of this study was to determine the prevalence tax of Oxyuris equi and concomitant clinical signs in horses of the Equestrian Center of the Third Regiment of Guard Cavalry in Porto Alegre, Rio Grande do Sul. Between August and October of 2017, 93 sport horses were evaluated, of variable races, with individual stalls and exercise regimen with various intensities. The evaluated variables were: general condition of the fur coat and tail, of the perianal region and imprint of the perianal region with adhesive tape throughout Graham’s method. The prevalence tax was 25,81% (24/93) and it related to clinical signs of opaque fur coat and tail hair loss in 10,75% (10/93) and with the presence of egg masses of in 2,15% (2/93).