The importance of considering age when quantifying wild animals' welfare

Epigenetic clocks, sex markers and age-class diagnostics in three harvested large mammals

The development of epigenetic clocks, or the DNA methylation-based inference of age, is an emerging tool for ageing in free ranging populations. In this study, we developed epigenetic clocks for three species of large mammals that are the focus of extensive management throughout their range in North America: white-tailed deer, black bear and mountain goat. We quantified differential DNA methylation patterns at over 30,000 cytosine-guanine sites (CpGs) from tissue samples of all three species (black bear n = 49; white-tailed deer n = 47; mountain goat n = 45). We used a penalized regression model (elastic net) to build explanatory (black bear r = .95; white-tailed deer r = .99; mountain goat r = .97) and robust (black bear Median Absolute Error or MAE = 1.33; white-tailed deer MAE = 0.29; mountain goat MAE = 0.61) models of age or clocks. We also characterized individual CpG sites within each species that demonstrated clear differences in methylation levels between age classes and sex, which can be used to develop a suite of accessible diagnostic markers. This tool has the potential to contribute to wildlife monitoring by providing easily obtainable representations of age structure in managed populations.

A cost-effective blood DNA methylation-based age estimation method in domestic cats, Tsushima leopard cats (Prionailurus bengalensis euptilurus) and Panthera species, using targeted bisulphite sequencing and machine learning models

Individual age can be used to design more efficient and suitable management plans in both in situ and ex situ conservation programmes for targeted wildlife species. DNA methylation is a promising marker of epigenetic ageing that can accurately estimate age from small amounts of biological material, which can be collected in a minimally invasive manner. In this study, we sequenced five targeted genetic regions and used 8-23 selected CpG sites to build age estimation models using machine learning methods at only about $3-7 per sample. Blood samples of seven Felidae species were used, ranging from small to big, and domestic to endangered species: domestic cats (Felis catus, 139 samples), Tsushima leopard cats (Prionailurus bengalensis euptilurus, 84 samples) and five Panthera species (96 samples). The models achieved satisfactory accuracy, with the mean absolute error of the most accurate models recorded at 1.966, 1.348 and 1.552 years in domestic cats, Tsushima leopard cats and Panthera spp. respectively. We developed the models in domestic cats and Tsushima leopard cats, which were applicable to individuals regardless of health conditions; therefore, these models are applicable to samples collected from individuals with diverse characteristics, which is often the case in conservation. We also showed the possibility of developing universal age estimation models for the five Panthera spp. using only two of the five genetic regions. We do not recommend building a common age estimation model for all the target species using our markers, because of the degraded performance of models that included all species.

Capturing wild animal welfare: a physiological perspective

Affective states, such as emotions, are presumably widespread across the animal kingdom because of the adaptive advantages they are supposed to confer. However, the study of the affective states of animals has thus far been largely restricted to enhancing the welfare of animals managed by humans in non-natural contexts. Given the diversity of wild animals and the variable conditions they can experience, extending studies on animal affective states to the natural conditions that most animals experience will allow us to broaden and deepen our general understanding of animal welfare. Yet, this same diversity makes examining animal welfare in the wild highly challenging. There is therefore a need for unifying theoretical frameworks and methodological approaches that can guide researchers keen to engage in this promising research area. The aim of this article is to help advance this important research area by highlighting the central relationship between physiology and animal welfare and rectify its apparent oversight, as revealed by the current scientific literature on wild animals. Moreover, this article emphasises the advantages of including physiological markers to assess animal welfare in the wild (e.g. objectivity, comparability, condition range, temporality), as well as their concomitant limitations (e.g. only access to peripheral physiological markers with complex relationships with affective states). Best-practice recommendations (e.g. replication and multifactorial approaches) are also provided to allow physiological markers to be used most effectively and appropriately when assessing the welfare of animals in their natural habitat. This review seeks to provide the foundation for a new and distinct research area with a vast theoretical and applied potential: wild animal welfare physiology.

Long-Tailed Macaque (Macaca fascicularis) Contraception Methods: A Systematic Review

The contraception-based approach to wildlife management is a humane and effective alternative to population control methods. Wildlife management only has a few conventional ways to control overpopulation, such as culling, translocation, poisoning, and allowing natural death. Nevertheless, these methods usually have short-term, lethal, and unethical effects. The present systematic review aims to review the knowledge on contraception reported in long-tailed macaques as an alternative to population control. We obtained 719 records from searching CABI, PubMed, ScienceDirect, and Scopus electronic databases. After the screening and selection process, according to PRISMA guidelines, 19 articles that met the eligibility criteria were chosen. Of the 19 articles, 15 were studies on female long-tailed macaque contraception methods (six (6) hormonal and nine (9) non-hormonal). We analyzed four (4) selected articles on male Cynomolgus monkey contraception methods (two (2) hormonal and two (2) non-hormonal). One of the nine (9) articles on female long-tailed macaque contraception reports negative results. Furthermore, only two (2) studies used free-ranging long-tailed macaques as test subjects, while seventeen (17) tested on captive ones. The challenges of long-tailed macaque contraception identified in this review were the effectiveness of the contraceptive, the administration route, the economic feasibility, the distinction between captive and free-ranging Cynomolgus macaques, the choice of permanent or reversible contraception, the capability of contraceptive use for population control, and the lack of studies on the free-ranging long-tailed macaque. Notwithstanding the literature gap on long-tailed macaque contraception for population control, long-tailed macaque contraception exhibits potential as an alternative method to culling long-tailed macaque. Future research should address these obstacles to support the long-tailed macaque contraception as an alternative population control method.

Investigating the Market Value of Brumbies (Equus caballus) in the Australian Riding Horse Market

Feral horses, also known as brumbies, are widely distributed across Australia with some populations being managed largely by human intervention. Rehoming of suitable feral horses following passive trapping has wide community acceptance as a management tool. However, there is little information about the number and relative economic value of feral horses compared with cohorts in the riding horse market. We examined 15,404 advertisements of horses for sale in 53 editions of Horse Deals, published from February 2017 to July 2022. Despite the considerable media attention and public scrutiny surrounding feral horse management, rehomed feral horses represented only a tiny fraction of the horse market in the current study. Of the 15,404 advertisements examined, only 128 (0.0083%) were for feral horses. We recorded phrases used to describe behavioural characteristics and other variables. The following variables were found to be not independent: Ridden Status, Height, Age, Sex, Colour, and Warning terms/more work. Using descriptive statistics to describe basic features of the data, the average price for feral horses ($1408) was lower than that for domestic horses ($1790) with the maximum price for a domestic horse being nearly twice the maximum for a feral horse. Univariate analysis showed feral horses were over-represented among "Unbroken" horses and underrepresented among "Ridden", "Broodmare" and "Harness" horses compared with domestic bred horses (p < 0.001). Feral horses appeared over-represented at shorter heights, among younger age groups (3 years or younger and 3.1 to 6 years) (p < 0.001) and in the dilute colour category (p = 0.008). The multivariable mixed model on price revealed that for domestic horses, the highest estimated marginal mean price averaged across the colour categories was for ridden horses aged 6.1-10-year-old at $1657.04 (95% CI $1320.56-$2074.66). In contrast, for feral horses, the multivariable mixed model demonstrated the similar highest estimated marginal mean averaged was for green broken 3-6-year-old horses that have undergone foundation training under saddle at $2526.97 (95% CI $1505.63-$4208.27). Australian feral horses were valued differently tfromsimilar domestic horses in the recreational riding horse market and further research is warranted to determine appropriate target markets and boost the sustainability of rehoming as a feral horse management tool.

Global gaps in age data based on skeletochronology for amphibians

Individual age and population age composition are the major concerns of ecologists, evolutionary biologists and conservation biologists. In amphibians, skeletochronology-counting the number of lines of arrested growth deposited in the bone tissue, is the dominant method to determine actual age of an individual. Since 1970s, age data of the ectothermic taxa have been accumulated and increasingly used in comparative studies. Here we make a global assessment for the availability of the data, based on a collection of 369 published papers. For a specific species, more males than females were sampled. Among the extant 8146 amphibian species, only 266 (3.3%) have been skeletochronologically investigated. Of these studied species, 2 (0.9% of 214) belong to caecilians, 56 (7.6% of 740) salamanders and 208 (2.9% of 7192) anurans. A complete paucity of data was seen in 80%, 50%, and 54% of families in the corresponding orders. More temperate species than tropical species were sampled, while the proportion of Palearctic species studied was higher than that in the other 5 biogeographical realms. Species inhabiting semi-aquatic niche were more likely to be studied than fossorial or plant dwellers. Age information of multiple populations (2-48) was available for species with a broad distribution, accounts for 61% of salamander and 43% of anuran species studied. Because these gaps in demographic knowledge can limit our understanding of questions ranging from life history evolution, population dynamics to conservation, we encourage herpetologists to pay more efforts on filling them.