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Background Animal identification is a topic of many studies, with a range of biometric methods currently in use. The cattle muzzle serves as a unique source of biometric traits. Objectives The aim of this study was to determine the best method for muzzle visualisation using imprints, the most frequent forms and minutiae points on imprints, and the minimum number of minutiae points required to establish an identity profile. Methods Noseprints of 30 calves were taken on different surfaces and visualised using different methods (white paper and cardboard/ninhydrin solution and glass tile/small particle reagents and ceramic tile/fluorescent powder and glossy photopaper/grey instant or magnetic powder). The imprint of the entire muzzle was photographed and analysed using the Automated Fingerprint Identification System (AFIS) to detect the most frequent forms based on friction ridges and minutiae points. Further mathematical simulation revealed the minimal number of points required for animal identification. Results The best imprint was obtained on glossy black photopaper with grey instant powder. After analysing the digitised images with the AFIS magnifier, the six forms of beads and ridges in the selected 12 minutiae points were detected, thus creating an identity chart. Computer simulation confirmed that the lowest number of minutiae points necessary for unique animal identification, and 0% possibility of form repetition at points, was nine of the 12 selected points. Conclusion As a biometric method, the muzzle imprint in combination with AFIS has the potential to be stored on large scale and used internationally, enabling identity control that is not susceptible to the issues involved with other biometric methods. Fingerprint technology with forensic methods and Automated Fingerprint Identification System (AFIS) was used for analyses of cows' muzzle imprint, revealing six specific forms in 12 minutiae points, out of which nine proved to be enough for identification, providing basis for this technology in animal identity control systems.

Background China is the birthplace of the deer family and the country with the most abundant deer resources. However, at present, China’s deer industry faces the problem that pure sika deer and hybrid deer cannot be easily distinguished. Therefore, the development of a SNP identification chip is urgently required. Results In this study, 250 sika deer, 206 red deer, 23 first-generation hybrid deer (F1), 20 s-generation hybrid deer (F2), and 20 third-generation hybrid deer (F3) were resequenced. Using the chromosome-level sika deer genome as the reference sequence, mutation detection was performed on all individuals, and a total of 130,306,923 SNP loci were generated. After quality control filtering was performed, the remaining 31,140,900 loci were confirmed. From molecular-level and morphological analyses, the sika deer reference population and the red deer reference population were established. The Fst values of all SNPs in the two reference populations were calculated. According to customized algorithms and strict screening principles, 1000 red deer-specific SNP sites were finally selected for chip design, and 63 hybrid individuals were determined to contain red deer-specific SNP loci. The results showed that the gene content of red deer gradually decreased in subsequent hybrid generations, and this decrease roughly conformed to the law of statistical genetics. Reaction probes were designed according to the screening sites. All candidate sites met the requirements of the Illumina chip scoring system. The average score was 0.99, and the MAF was in the range of 0.3277 to 0.3621. Furthermore, 266 deer (125 sika deer, 39 red deer, 56 F1, 29 F2,17 F3) were randomly selected for 1 K SNP chip verification. The results showed that among the 1000 SNP sites, 995 probes were synthesized, 4 of which could not be typed, while 973 loci were polymorphic. PCA, random forest and ADMIXTURE results showed that the 1 K sika deer SNP chip was able to clearly distinguish sika deer, red deer, and hybrid deer and that this 1 K SNP chip technology may provide technical support for the protection and utilization of pure sika deer species resources. Conclusion We successfully developed a low-density identification chip that can quickly and accurately distinguish sika deer from their hybrid offspring, thereby providing technical support for the protection and utilization of pure sika deer germplasm resources.

Abstract The camel industry uses traditional (i.e., iron brands and ear tags) and modern (i.e., microchips) identification (ID) systems without having performance results of reference. Previously iron-branded (n = 45; 1 yr) and microchipped (n = 59; 7 yr) camels showed problems of healing (8.6% of brands) and reading (only 42.9% of brands and 69.5% of microchips were readable), which made their use inadvisable. With the aim of proposing suitable ID systems for different farming conditions, an on-field study was performed using a total of 528 dromedaries at 4 different locations (Egypt, n = 83; Spain, n = 304; Saudi Arabia, n = 90; and Tunisia, n = 51). The ID devices tested were visual (button ear tags, 28.5 mm diameter, n = 178; double flag ear tags, 50 by 15 mm, n = 83; both made of polyurethane) and electronic (ear tags, n = 90, and rumen boluses, n = 555). Electronic ear tags were polyurethane-loop type (75 by 9 mm) with a container in which a 22-mm transponder of full-duplex technology was lodged. Electronic boluses of 7 types, varying in dimensions (50 to 76 mm length, 11 to 21 mm width, and 12.7 to 82.1 g weight) and specific gravity (SG; 1.49 to 3.86) and each of them containing a 31-mm transponder of half-duplex technology, were all administered to the dromedaries at the beginning of the study. When a low-SG bolus was lost, a high-SG bolus was readministered. Readability rates of each ID system were evaluated during 1 to 3 yr, according to device and location, and yearly values were estimated for comparison. On a yearly basis, visual ear tag readability was not fully satisfactory; it was lower for rectangular ear tags (66.3%) than for button ear tags (80.9%). Yearly readability of electronic ear tags was 93.7%. Bolus readability dramatically varied according to their SG; the SG < 2.0 boluses were fully lost after 8 mo. In contrast, the SG > 3.0 boluses were efficiently retained (99.6 to 100%) at all locations. In conclusion, according to the expected long lifespan of camels, low ID performances were observed for iron brands, injectable microchips, and ear tags (visual and electronic), making their use inadvisable as unique ID systems in camels. The high readability of dense electronic boluses recommended their use as a permanent ID device of reference in camels.

New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery,determine howmany species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens (20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94–407 bp).We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process,Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly,we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (200 bp). Only very short mini-barcodes (200 bp) perform poorly, especially when they are located near the 5 end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes >200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for reexamination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.

Despite the ubiquity of parasites and pathogens, behavioral and physiological responses to infection vary widely across individuals. Although such variation can have pronounced effects on population-level processes, including the transmission of infectious disease, the study of individual responses to infection in free-living animals remains a challenge. To fully understand the causes and consequences of heterogeneous responses to infection, research in ecoimmunology and disease-ecology must incorporate minimally invasive techniques to track individual animals in natural settings. Here, we review how several technologies, collectively termed remote biomonitoring, enable the collection of data on behavioral and physiological responses to infection in small, free-living animals. Specifically, we focus on the use of radiotelemetry and radio-frequency identification to study fever, sickness-behaviors (including lethargy and anorexia), and rates of inter-individual contact in the wild, all of which vary widely across individuals and impact the spread of pathogens within populations. In addition, we highlight future avenues for field studies of these topics using emerging technologies such as global positioning system tracking and tri-axial accelerometry. Through the use of such remote biomonitoring techniques, researchers can gain valuable insights into why responses to infection vary so widely and how this variation impacts the spread and evolution of infectious diseases.

Video-based monitoring is essential nowadays in cattle farm management systems for automated evaluation of cow health, encompassing body condition scores, lameness detection, calving events, and other factors. In order to efficiently monitor the well-being of each individual animal, it is vital to automatically identify them in real time. Although there are various techniques available for cattle identification, a significant number of them depend on radio frequency or visible ear tags, which are prone to being lost or damaged. This can result in financial difficulties for farmers. Therefore, this paper presents a novel method for tracking and identifying the cattle with an RGB image-based camera. As a first step, to detect the cattle in the video, we employ the YOLOv8 (You Only Look Once) model. The sample data contains the raw video that was recorded with the cameras that were installed at above from the designated lane used by cattle after the milk production process and above from the rotating milking parlor. As a second step, the detected cattle are continuously tracked and assigned unique local IDs. The tracked images of each individual cattle are then stored in individual folders according to their respective IDs, facilitating the identification process. The images of each folder will be the features which are extracted using a feature extractor called VGG (Visual Geometry Group). After feature extraction task, as a final step, the SVM (Support Vector Machine) identifier for cattle identification will be used to get the identified ID of the cattle. The final ID of a cattle is determined based on the maximum identified output ID from the tracked images of that particular animal. The outcomes of this paper will act as proof of the concept for the use of combining VGG features with SVM is an effective and promising approach for an automatic cattle identification system

Multirotor drones have been one of the most important technological advances of the last decade. Their mechanics are simple compared to other types of drones and their possibilities in flight are greater. For example, they can take-off vertically. Their capabilities have therefore brought progress to many professional activities. Moreover, advances in computing and telecommunications have also broadened the range of activities in which drones may be used. Currently, artificial intelligence and information analysis are the main areas of research in the field of computing. The case study presented in this article employed artificial intelligence techniques in the analysis of information captured by drones. More specifically, the camera installed in the drone took images which were later analyzed using Convolutional Neural Networks (CNNs) to identify the objects captured in the images. In this research, a CNN was trained to detect cattle, however the same training process could be followed to develop a CNN for the detection of any other object. This article describes the design of the platform for real-time analysis of information and its performance in the detection of cattle.

Electronic identification of animals has become increasingly important worldwide to improve and ensure traceability. In warm and hot climates, such as Brazil, boluses can have advantages over ear tags as the internal devices reduce the risks of ear tag losses, tissue damage, and lesions on the ear. Electronic boluses, however, are often perceived as having negative characteristics, including reported difficulties of administration in small ruminants. This paper describes the factors associated with bolus design that affect the swallowing of a bolus in sheep. Other factors that might influence bolus swallowing time have also been considered. In addition, the effect of bolus design on its performance was evaluated. A total of 56 Suffolk ewes were used to assess the ease of administration and retention of 3 types of electronic ruminal boluses (mini, 11.5 × 58.0 mm and 21.7 g; small, 14.8 × 48.5 mm and 29.5 g; standard, 19.3 × 69.8 mm and 74.4 g) during a whole productive year, including pregnancy and lamb suckling. Ewe age (5.6 ± 2.3 yr) and weight (85.07 ± 8.2 kg BW) were recorded, as well as time for bolus swallowing. The deglutition of the bolus and any resulting blockages in the esophagus were monitored by visual observations. Retention and readability of the boluses were regularly monitored for d 1, wk 1, mo 1, and every mo until 1 yr. Time for bolus swallowing differed substantially with bolus type and was greater (P < 0.05) for the standard bolus (32.8 ± 6.9 s) when compared to small and mini boluses, which did not differ (8.5 ± 2.0 vs. 9.2 ± 2.7 s; P > 0.05). The bolus o.d. and length were positively correlated with swallowing time (P < 0.01). The ewe weight was negatively correlated with swallowing time (P < 0.05). At 6 mo all electronic boluses showed 100% retention rate, and at 12 mo, bolus retention was 100%, 94.5%, and 100% for mini, small, and standard boluses, respectively (P > 0.05). At 12 mo, all boluses showed 100% readability, except for small boluses, which had a readability of 94.5%. In conclusion, bolus design affected swallowing time and bolus readability. A reduction in boluses length and o.d. needs to be carried out to provide ease of administration and for boluses to be used as an effective means of electronic identification. Therefore, this study shows that adequately designed boluses are safe and suitable for identifying adult sheep and can therefore be used in hot climates.

In amphibian capture-recapture studies, commonly used individual-identification methods include toe clipping as well as less invasive alternatives of varying cost. Yet, choosing the best method for a study is challenging, because both the reliability for identification and the severity of adverse effects of a given mark type can greatly vary between species as well as life stages. We compared the reliability of three identification methods in young agile frogs ( Rana dalmatina ): clipping a single phalanx, injecting visible-implant-elastomer (VIE) tags (one of six colours) under the skin, and photo-based identification using natural colouration. Individuals were regularly photographed from the start of metamorphosis onwards, and were marked by the other two methods soon after all of them finished metamorphosis. Subsequently, we checked mark retention by each method multiple times for more than a year. Photo-based identification was far more reliable than the other two methods: 100% identification success post-metamorphosis in all checking events within small housing groups, and 98% with computer-assisted identification across all housing groups. Post-metamorphic body colouration remained largely stable, and the major patterns were already present at metamorphosis. Based on VIE colour alone, we could correctly identify the animals in 77% of the checks. Green tags were the easiest to recognize. VIE often broke into smaller parts, and those were sometimes found only outside the originally tagged body part (15%) or not found at all (10%). VIE was better retained in the legs than in the arms. Dissection revealed that migrating VIE pieces can accumulate in the internal organs, especially the kidneys. The clipped toe tip was successfully recognized only in 41% of checks. We conclude that photo-based identification is superior to both VIE-tagging and toe tipping in young agile frogs, and this method should be preferred in future studies seeking a cost-efficient yet reliable identification method in this species.

Dairy goat kids born during a 3-yr period (n=97) and their mothers (n=29) were used for a long-term evaluation of the performance of 9 types of identification (ID) devices. Kids wore multiple ID devices: visual ear tags (V1, tip-tag, n=47; V2, official, n=50), electronic ear tags (E1, button-button, n=46; E2, flag-button, n=46), electronic rumen boluses (B1, mini-bolus 14g, n=92; B2, mini-bolus 20g, n=28; B3, standard bolus 75g, n=34) and glass-encapsulated transponders injected in the forefeet (T1, 15mm, n=75; T2, 12mm, n=100). Visual ear tags were applied at birth and removed in yearlings, whereas electronic ear tags were applied after bolusing with B1 (6.7kg BW and 30 d, on average); B2 were administered in the event of a B1 loss, and B3 in case of a B2 loss and in goat does. At d 60 of age, kids were allocated into 2 groups to evaluate the effects of rearing system on ID. Treatments were: weaned (n=46), and not weaned (n=46) where kids suckled a milk substitute until d 150. Readability of ID devices (read/readable×100) was monitored from 1 to 3 yr of age, depending on device and year of birth. Long-term readability was analyzed using a nonparametric survival analysis. A total of 3.3% infections and 6.5% tissue reactions were reported for electronic ear tags, but ears were fully healed in yearlings. Weaning numerically reduced B1 losses at d 150 (weaned, 84.8% vs. not weaned, 73.3%). Readability of visual ear tags in yearlings (V1, 82.9%; V2, 94.0%) was lower than for electronic ear tags (E1 and E2, 100%). Mini-bolus readability in yearlings did not differ by type (B1, 71.4%; B2, 84.6%) or with visual ear tags. No effect of inject type was reported (T1, 92.0%; T2, 96.0%). Survival analysis after yr 3 gave the greatest readability value for E1 (100%), which did not differ from B3 (96.8%). The lowest readability was estimated for B1 (66.3%), followed by E2 (79.8%), B2 (81.4%), and T1 (90.4%). In conclusion, button-button electronic ear tags and standard boluses were the more efficient devices under our conditions, their readability values being greater than injects, electronic mini-boluses, and visual and flag-button electronic ear tags. Transponders injected in the forefeet and mini-boluses used here are not recommended in practice. Further research on E1 and B3 electronic devices should be done in a higher number of goats to confirm the current results.