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.

The Sarcoptic Mange in Maned Wolf (Chrysocyon brachyurus): Mapping an Emerging Disease in the Largest South American Canid

The maned wolf (Chrysocyon brachyurus) is the largest South American canid. In Brazil, as in other countries, it is considered an endangered species. Habitat loss, landscape changes, hunting, and roadkill are the main threats to this species. In addition, invasive diseases of domestic animals are considered to be an emerging threat to the maned wolf, where parasitic diseases are relevant. Sarcoptic mange is a skin disease caused by the mite Sarcoptes scabiei. This disease is currently almost globally distributed, with a remarkable host diversity. In Brazil, reports of sarcoptic mange in wildlife include several species, both wild and captive. However, the impact of this disease on wildlife is unknown. At the time of writing, there is only one published report of sarcoptic mange in maned wolves. This study sheds light on the occurrence of sarcoptic mange in free-ranging maned wolves in their natural range. A total of 52 cases (suspected and confirmed) of sarcoptic mange were identified through social media review, camera trapping, chemical immobilization and sample collection. These cases were distributed in southeastern Brazil, in the states of São Paulo (n = 34), Minas Gerais (n = 17), and Rio de Janeiro (n = 1), demonstrating a rapid and widespread spread of this disease, although it still only occurs in part of the species' range. We expect that these results will help to subsidize future actions relevant to the control of this emerging disease.

Widespread Exposure to Mosquitoborne California Serogroup Viruses in Caribou, Arctic Fox, Red Fox, and Polar Bears, Canada

Northern Canada is warming at 3 times the global rate. Thus, changing diversity and distribution of vectors and pathogens is an increasing health concern. California serogroup (CSG) viruses are mosquitoborne arboviruses; wildlife reservoirs in northern ecosystems have not been identified. We detected CSG virus antibodies in 63% (95% CI 58%-67%) of caribou (n = 517), 4% (95% CI 2%-7%) of Arctic foxes (n = 297), 12% (95% CI 6%-21%) of red foxes (n = 77), and 28% (95% CI 24%-33%) of polar bears (n = 377). Sex, age, and summer temperatures were positively associated with polar bear exposure; location, year, and ecotype were associated with caribou exposure. Exposure was highest in boreal caribou and increased from baseline in polar bears after warmer summers. CSG virus exposure of wildlife is linked to climate change in northern Canada and sustained surveillance could be used to measure human health risks.

Tularemia above the Treeline: Climate and Rodent Abundance Influences Exposure of a Sentinel Species, the Arctic Fox (Vulpes lagopus), to Francisella tularensis

Tularemia is a zoonotic disease found throughout most of the northern hemisphere that may experience range expansion with warming temperatures. Rodents and lagomorphs are reservoirs for the disease, and outbreaks of tularemia often follow peaks in their abundance. As small mammals dominate the diet of arctic foxes (Vulpes lagopus), we determined whether they may serve as sentinels by identifying antibodies in live-captured and harvested foxes from northern Canada. Overall seroprevalence was 2% (CI95 1-2%) in 176 foxes harvested in 2018-2019 compared to 17% (CI95 12-22%) of 230 foxes captured live in 2011-2021. Prevalence was at an all-time high in 2018, following a peak in vole abundance in 2017. Antibodies were identified in fox pups born in 2018 and 2019, suggesting that F. tularensis was actively transmitted during the summers. High precipitation during the summer, increased snow cover and colder temperatures in May, and a higher abundance of voles were all associated with increased seroprevalence in live-captured foxes. Thus, exposure to F. tularensis is largely mediated through climate and rodent populations in the Canadian Arctic, and arctic foxes are useful sentinels for F. tularensis in northern ecosystems. Further studies should investigate whether infection impacts arctic fox survival and reproductive success in the circumpolar North.

Canine morphometrics as a tool for distinguishing species, sex, and age class in Southern Ocean fur seals

Carcasses resulting from natural mortalities are invaluable for use in scientific studies, provided species, sex, and age class are known. When such data are unavailable, identifying skeletal remains is necessary if one is to use the information contained within samples. Teeth are amongst the best preserved skeletal remains owing to the durability of enamel and dentine. Here, we tested whether external measurements of canines could be used to distinguish two partially sympatric species of Southern Ocean fur seals, the Antarctic Arctocephalus gazella and Sub-Antarctic A. tropicalis fur seals. We also investigated whether the external measurements of canines could be used to determine the age, sex, as well as island of origin of the animals. Eight morphological variables (crown length, root length, crown width, root width, crown thickness, root thickness, total canine length, and count of external surface annular ridges) were recorded from canines of 340 individuals of known species, sex, and island of origin. The count of external annular ridges provided a good estimate of age, which was confirmed by counting the growth layer groups of sectioned teeth, especially for older animals (> 9 years old). External canine measurements proved useful in distinguishing species, as well as sex within and between species, particularly in adult animals. Species were more difficult to distinguish in females than in males. The islands of origin could only be inferred in male Antarctic fur seals. This study indicates that fur seal teeth of unknown provenance, found either in breeding colonies or as vagrants, provide evidence on species, sex, and age of the animal, which increases the value of associated samples. It further highlights the importance of external measurements of skeletal remains such as canine teeth in separating closely related species.

Are foxes (Vulpes spp.) good sentinel species for Toxoplasma gondii in northern Canada?

BACKGROUND

In changing northern ecosystems, understanding the mechanisms of transmission of zoonotic pathogens, including the coccidian parasite Toxoplasma gondii, is essential to protect the health of vulnerable animals and humans. As high-level predators and scavengers, foxes represent a potentially sensitive indicator of the circulation of T. gondii in environments where humans co-exist. The objectives of our research were to compare serological and molecular assays to detect T. gondii, generate baseline data on T. gondii antibody and tissue prevalence in foxes in northern Canada, and compare regional seroprevalence in foxes with that in people from recently published surveys across northern Canada.

METHODS

Fox carcasses (Vulpes vulpes/Vulpes lagopus, n = 749) were collected by local trappers from the eastern (Labrador and Québec) and western Canadian Arctic (northern Manitoba, Nunavut, and the Northwest Territories) during the winters of 2015-2019. Antibodies in heart fluid were detected using a commercial enzyme-linked immunosorbent assay. Toxoplasma gondii DNA was detected in hearts and brains using a magnetic capture DNA extraction and real-time PCR assay.

RESULTS

Antibodies against T. gondii and DNA were detected in 36% and 27% of foxes, respectively. Detection of antibodies was higher in older (64%) compared to younger foxes (22%). More males (36%) than females (31%) were positive for antibodies to T. gondii. Tissue prevalence in foxes from western Nunavik (51%) was higher than in eastern Nunavik (19%). At the Canadian scale, T. gondii exposure was lower in western Inuit regions (13%) compared to eastern Inuit regions (39%), possibly because of regional differences in fox diet and/or environment. Exposure to T. gondii decreased at higher latitude and in foxes having moderate to little fat. Higher mean infection intensity was observed in Arctic foxes compared to red foxes. Fox and human seroprevalence showed similar trends across Inuit regions of Canada, but were less correlated in the eastern sub-Arctic, which may reflect regional differences in human dietary preferences.

CONCLUSIONS

Our study sheds new light on the current status of T. gondii in foxes in northern Canada and shows that foxes serve as a good sentinel species for environmental circulation and, in some regions, human exposure to this parasite in the Arctic.

Epigenetic Measurement of Key Vertebrate Population Biology Parameters

The age, sex, and sexual maturity of individual animals are key parameters in assessing wild populations and informing conservation management strategies. These parameters represent the reproductive potential of a population and can indicate recovery rates or vulnerabilities. Natural populations of wild animals are difficult to study; logistically, economically, and due to the impacts of invasive biomonitoring. Genetic and epigenetic analyses offer a low impact, low cost, and information-rich alternative. As epigenetic mechanisms are intrinsically linked with both biological aging and reproductive processes, DNA methylation can be used as a suitable biomarker for population biology study. This review assesses published research utilizing DNA methylation analysis in relation to three key population parameters: age, sex, and sexual maturity. We review studies on wild vertebrates that investigate epigenetic age relationships, with successful age estimation assays designed for mammals, birds, and fish. For both determination of sex and identification of sexual maturity, very little has been explored regarding DNA methylation-based assays. Related research, however, confirms the links between DNA methylation and these processes. Future development of age estimation assays for underrepresented and key conservation taxa is suggested, as is the experimental development and design of DNA methylation-based assays for both sex and sexual maturity identification, further expanding the genomics toolkit for population biology studies.

Extensive daily movement rates measured in territorial arctic foxes

An animal's movement rate is a central metric of movement ecology as it correlates with its energy acquisition and expenditure. Obtaining accurate estimates of movement rate is challenging, especially in small highly mobile species where GPS battery size limits fix frequency, and geolocation technology limits positions' precision. In this study, we used high GPS fix frequencies to evaluate movement rates in eight territorial arctic foxes on Bylot Island (Nunavut, Canada) in July-August 2018. We also assessed the effects of fix interval and location error on estimated movement rates. We obtained 96 fox-days of data with a fix interval of 4 min and 12 fox-days with an interval of 30 s. We subsampled the latter dataset to simulate six longer fix intervals ranging from 1 to 60 min and estimated daily distances traveled by adding linear distances between successive locations. When estimated with a fix interval of 4 min, daily distances traveled by arctic foxes averaged 51.9 ± 11.7 km and reached 76.5 km. GPS location error averaged 11 m. Daily distances estimated at fix intervals longer than 4 min were greatly underestimated as fix intervals increased, because of linear estimation of tortuous movements. Conversely, daily distances estimated at fix intervals as small as 30 s were likely overestimated due to location error. To our knowledge, no other territorial terrestrial carnivore was shown to routinely travel daily distances as large as those observed here for arctic foxes. Our results generate new hypotheses and research directions regarding the foraging ecology of highly mobile predators. Furthermore, our empirical assessment of the effects of fix interval and location error on estimated movement rates can guide the design and interpretation of future studies on the movement ecology of small opportunistic foragers.

Updates on the Morphometric Characterization of Indian Pangolin (Manis crassicaudata) in Sri Lanka

An accurate morphological description and analysis based on reliable data are unavailable for the geographically isolated population of M. crassicaudata in Sri Lanka. This study provides the most updated morphological description of M. crassicaudata with special reference to body measurements directly obtained from 27 specimens collected island-wide. Morphological parameters were recorded under three age classes that were defined based on their body weight (BW) and total body length (TBL); juvenile (BW: <4.3 kg TBL: <56.0 cm), subadult (BW: 4.3-7.3 kg TBL: 56-101 cm), and adult (BW: >7.3 kg TBL: >101 cm) and gender to reveal sexual dimorphism based on morphometric parameters. The TBL of adult males ranged between 137 and 177 cm while body weight ranged between 20.4 and 48.8 kg. The average count of body scales was 511 ± 21. The body scales were found arranged in 13 longitudinal rows with the highest number of scales observed on the vertebral scale row (16 ± 1). Three major scale morphs were identified; broad rhombic scales, elongated kite-shaped scales, and folded shaped scales. Broad rhombic shaped scales was the dominant scale type (80.49%) on the body (405 ± 7). The tail-length to body-length ratio of an Indian pangolin was 0.87. The tail length of an Indian pangolin is a reliable predictor of the TBL and has potential implications in quick field data gathering.

Pulsed food resources affect reproduction but not adult apparent survival in arctic foxes

As top or mesopredators, carnivores play a key role in food webs. Their survival and reproduction are usually thought to be influenced by prey availability. However, simultaneous monitoring of prey and predators is difficult, making it challenging to evaluate the impacts of prey on carnivores' demography. Using 13 years of field data on arctic foxes Vulpes lagopus in the Canadian High Arctic and a capture-recapture multi-event statistical approach, we investigated the hypothesis that increases in lemming abundance (a cyclic and unpredictable food source) and goose colony proximity (a stable but spatially and temporally limited food source) would be associated with increased apparent survival and reproduction probabilities of adults. Adult apparent survival varied greatly across years (0.13-1.00) but was neither affected by lemming nor goose variations in abundance. However, reproduction probabilities were strongly influenced by both lemming abundance and access to the goose colony. A fox breeding in the best conditions of food availability (year of high lemming density inside the goose colony) had a reproduction probability four times higher than one experiencing the worst conditions (year of low lemming density outside the goose colony). Breeding status of individuals also played a role, with breeders having a 10-20% higher probability of survival and 30% higher probability of reproduction the following year than non-breeders. As the Arctic ecosystem changes due to increased temperatures and species ranges, this study will allow better predictions of predator responses to management or environmental changes and a better understanding of ecosystem functioning.

Assessment of the global pattern of genetic diversity in Echinococcus multilocularis inferred by mitochondrial DNA sequences

The aim of this review was to assess our current knowledge on phylogeography and global genetic structure of Echinococcus multilocularis populations originating from rodents, wild canid hosts, and human. Six bibliographic databases were searched from 1990 to 2017, identifying a total of 110 publications. The cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) sequences of E. multilocularis from Asia, Europe, and North Americas were analyzed to estimate the diversity and neutrality indices, and genetic differentiation. A total of 69 (cox1, 36.7%) and 16 haplotypes (cytb, 19.2%) were grouped into various geographical clades. A parsimonious haplotype network demonstrated a star-like feature with haplo-groups Em2 (Asia: 36%), Em105 (Eastern Tibetan plateau: 4.8%), Em46 (Europe: 9.1%), Em73, (Europe: 2.7%) and Em92 (North Americas: 4.3%) as the most common haplotypes. A relatively high level of genetic diversity was detected in rodent-derived E. multilocularis isolates (Haplotype diversity: 0.944), wild canids (Hd: 0.912), and human origin (Hd: 0.704). The highest number of haplotypes (n = 59) and the highest haplotype diversity (0.969) were identified in the Asian and European populations, respectively. Cladistic phylogenetic tree indicated the European clade has a sister relationship with the Asian clade. However, some North American haplotypes were assigned to the European clade together with haplotypes from Poland. The statistically significant Fst values indicated that E. multilocularis populations of Asian-European, Asian-North American, and European-North American origins were genetically differentiated (Fst: 0.22624 to 0.43059). An occurrence of distinct parasite populations suggests that E. multilocularis derived from glacial refugia have been plausibly sustained by indigenous hosts during the Pleistocene Epoch.

Estimation of chimpanzee age based on DNA methylation

In wild animal conservation, knowing the age of an individual animal is extremely beneficial. However, estimating the age is difficult for many species. Recently, epigenetics-based methods of estimating age have been reported. These studies were predominantly on humans with few reports on other animals, especially wild animals. In the present study, a chimpanzee (Pan troglodytes) age prediction model was developed based on the ELOVL2, CCDC102B, and ZNF423 genes that may also have application in human age prediction. Pyrosequencing was used to measure methylation in 20 chimpanzee blood samples and correlation between age and methylation status was calculated. Age and methylation of sites in ELOVL2 and CCDC102B were significantly correlated and an age prediction model was created using these genes. In the regression equation using only ELOVL2, the highest correlation coefficient was 0.741, with a mean absolute deviation (MAD) of 5.41, compared with the combination of ELOVL2 and CCDC102B, where the highest correlation coefficient was 0.742 and the MAD was 5.41. Although larger MADs were observed in chimpanzees than in humans based on these genes, the results indicate the feasibility of estimating chimpanzee age using DNA methylation, and can have implications in understanding the ecology of chimpanzees and chimpanzee conservation.