Methylation-based markers for the estimation of age in African cheetah, Acinonyx jubatus

Age is a key demographic in conservation where age classes show differences in important population metrics such as morbidity and mortality. Several traits, including reproductive potential, also show senescence with ageing. Thus, the ability to estimate age of individuals in a population is critical in understanding the current structure as well as their future fitness. Many methods exist to determine age in wildlife, with most using morphological features that show inherent variability with age. These methods require significant expertise and become less accurate in adult age classes, often the most critical groups to model. Molecular methods have been applied to measuring key population attributes, and more recently epigenetic attributes such as methylation have been explored as biomarkers for age. There are, however, several factors such as permits, sample sovereignty, and costs that may preclude the use of extant methods in a conservation context. This study explored the utility of measuring age-related changes in methylation in candidate genes using mass array technology. Novel methods are described for using gene orthologues to identify and assay regions for differential methylation. To illustrate the potential application, African cheetah was used as a case study. Correlation analyses identified six methylation sites with an age relationship, used to develop a model with sufficient predictive power for most conservation contexts. This model was more accurate than previous attempts using PCR and performed similarly to candidate gene studies in other mammal species. Mass array presents an accurate and cost-effective method for age estimation in wildlife of conservation concern.

Biological clocks as age estimation markers in animals: a systematic review and meta-analysis

Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.

Museomics Provides Insights into Conservation and Education: The Instance of an African Lion Specimen from the Museum of Zoology “Pietro Doderlein”

Innovative technological approaches are crucial to enhance naturalistic museum collections and develop information repositories of relevant interest to science, such as threatened animal taxa. In this context, museomics is an emerging discipline that provides a novel approach to the enhancement and exploitation of these collections. In the present study, the discovery of a neglected lion skeleton in the Museum of Zoology “Pietro Doderlein” of the University of Palermo (Italy) offered the opportunity to undertake a multidisciplinary project. The aims of the study consisted of the following: (i) adding useful information for museographic strategies, (ii) obtaining a new genetic data repository from a vulnerable species, (iii) strengthening public awareness of wildlife conservation, and (iv) sharing new learning material. The remains of the lion were examined with a preliminary osteological survey, then they were restored by means of 3D printing of missing skeletal fragments. Phylogenetic analyses based on cytochrome b sequence clearly indicate that the specimen belongs to the Central Africa mitochondrial clade. At the end of the study, the complete and restored skeleton was exhibited, along with all of the information and data available from this project. This study shows a useful approach for the restoration and enhancement of a museum specimen, with important opportunities for preserving biodiversity and driving specific conservation policies, but also for providing Life Science learning material.

Age estimation of Tiger Panthera tigris (Linnaeus, 1758) and Lion Panthera leo (Linnaeus, 1758) (Mammalia: Carnivora: Felidae): applicability of cementum annuli analysis method

We describe the applicability of the cementum annuli analysis technique for estimating the age of Tiger Panthera tigris and Asiatic Lion Panthera leo using incisor teeth. We used I2 and I3 incisor teeth from the right mandible of Tiger and I2 and I3 from the left premaxilla of the Lion. The longitudinal sections of the teeth were prepared using an economical hand grinding technique with the help of sandpaper, followed by decalcification and staining with hematoxylin. Two cementum layers were observed under the microscope in each of the I2 and I3 incisor teeth of the Tiger and six cementum layers were observed in each of the I2 and I3 incisor teeth of the Lion. The permanent incisors in Tiger and Lion erupt between 12 and 14 months of age; hence, we added one year to the counted number of cementum layers to estimate the final age of Tiger and Lion incisors. The age of Tiger and Lion incisors were estimated to be of three years and seven years, respectively. This method may be suitable for estimating other carnivores’ age and applicable in wildlife forensic studies.

Low-Cost Forensics Reveal High Rates of Non-lethal Snaring and Shotgun Injuries in Zambia's Large Carnivores

The impact of snaring and human-wildlife conflict (HWC) on large carnivore populations is of growing concern, and yet few empirical data are available. Mortality is the metric most often used, but non-lethal injuries that impact fitness are also important threats. However, because non-lethal injuries to wild carnivores are difficult to detect, they have received little study. Using straightforward forensic examination of the skulls of trophy-hunted lions and leopards from Luangwa Valley (LV) and Greater Kafue Ecosystem (GKE), Zambia, we identified non-lethal injuries consisting of snare damage to teeth and shotgun pellets in skulls. Wire snare entanglement can cause permanent, diagnostic damage to carnivore teeth when individuals bite and pull on the wire. Shotguns are used by poachers, as well as during HWCs to drive off carnivores perceived as threats. Carnivores struck by shotgun pellets can suffer non-lethal, but potentially toxic injuries such as pellets embedded in their skulls. Because poaching and HWC are generally more prevalent near human settlements, we predicted a higher incidence of anthropogenic injuries to carnivores in Luangwa where the human population is larger and more concentrated along protected area edges than Kafue. Contrary to expectation, anthropogenic injuries were more prevalent among lions and leopards in Kafue than Luangwa. Notably, definitive evidence of snare entanglement greatly surpassed previous estimates for these regions. Overall, 37% (41 in 112) of adult male lions (29% in Luangwa, 45% in Kafue) and 22% (10 in 45) of adult male leopards (17% in Luangwa, 26% in Kafue) examined had survived being snared at some point in their lifetime. Among adult male lions, 27% (30 in 112) had old shotgun pellet injuries to their skulls. Our procedure of forensic examination of carnivore skulls and teeth, some of which can be applied to live-captured animals, allows for improved detection of cryptic, non-lethal anthropogenic injuries. Further, our methods represent a consistent and economical way to track changes in the frequency of such injuries over time and between regions, thereby providing a direct measure of the effectiveness of conservation programs that seek to reduce poaching and HWC.

Naturally-occurring tooth wear, tooth fracture, and cranial injuries in large carnivores from Zambia

Determining the incidence and causes of craniodental damage in wild carnivores is often constrained by limited access to specimens with associated ecological data, such as prey type and abundance. We assessed dental condition and cranial injuries in lion, leopard, and spotted hyena in relation to prey and predator populations in Zambia's Luangwa Valley, where large prey are more abundant and lion and leopard more numerous, and the Greater Kafue Ecosystem, where smaller prey species are more prevalent and lion and leopard less common. In Luangwa, lions had significantly higher rates of tooth fracture, and blunt trauma injuries attributable to prey-handling, compared to Kafue lions. In contrast, leopards in both regions had similar rates of tooth wear and breakage. Overall, lions showed a significantly higher tooth fracture rate than leopards on a per tooth basis. Spotted hyenas had the highest rates of tooth wear and fracture among all three carnivores, and greatly exceeded previously recorded rates based on historical samples. Despite larger numbers of lion and leopard in Luangwa, there was no difference in incidence of intraspecific injuries between regions. These results are consistent with a greater abundance of large prey species, especially buffalo, in the diets of Luangwa lions, and previous work showing a reliance on smaller prey species in Kafue throughout the large carnivore guild.