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.

Estimating age of mule deer in the field: Can we move beyond broad age categories?

Age of individuals is an intrinsic demographic parameter used in the modeling and management of wildlife. Although analysis of cementum annuli from teeth is currently the most accurate method used to age ungulates, the age of live ungulates in the field can be estimated by examining tooth wear and tooth replacement patterns. However, there may be limitations to aging based on tooth wear as the rate of tooth wear likely varies among individuals due to factors such as age, diet, environment, and sex. Our objective was to determine the reliability of estimating age for mule deer based on tooth wear and tooth replacement patterns. We compared ages estimated by tooth wear (collected at time of capture for a statewide monitoring effort) to ages determined from cementum analysis (from teeth collected after mortalities of radio-tracked animals from the monitoring effort). Accuracy was high; ages estimated from tooth wear were within one year of cementum ages >75% of the time when aged by experienced observers. Bias in accuracy for estimates of age was low but slightly biased toward underestimation (i.e., 0.6 years on average)-especially as cementum age increased. Our results indicate that aging mule deer using patterns in tooth wear can be reliable if observers estimating age have experience using this method.

Anthropogenic edge effects and aging errors by hunters can affect the sustainability of lion trophy hunting

Many large predator populations are in decline globally with significant implications for ecosystem integrity and function. Understanding the drivers of their decline is required to adequately mitigate threats. Trophy hunting is often cited as a tool to conserve large mammal populations but may also have negative impacts if not well managed. Here we use a spatially implicit, individual based model to investigate the threats posed to African lion populations by poorly managed trophy hunting and additive anthropogenic mortality such as poaching and retaliatory killing. We confirm the results of previous studies that show that lion trophy hunting can be sustainable if only older male lions are hunted, but demonstrate that hunting becomes unsustainable when populations are exposed to additional anthropogenic mortality, as is the case for most free ranging populations. We show that edge effects can be a critical determinant of population viability and populations that encompass well protected source areas are more robust than those without. Finally, errors in aging of hunted lions by professional trophy hunters may undermine the sustainability of the age-based quota setting strategies that are now widely used to manage lion trophy hunting. The effect of aging errors was most detrimental to population persistence in the ≥ 6 and ≥ 7 year-old age thresholds that are frequently used to define suitably aged lions for hunting. Resource managers should limit offtakes to older demographics and additionally take a precautionary approach when setting hunting quotas for large carnivore populations that are affected by other sources of anthropogenic mortality, such as bush-meat poaching, retaliatory killing and problem animal control.

Agricultural land use shapes dispersal in white-tailed deer (Odocoileus virginianus)

BACKGROUND

Dispersal is a fundamental process to animal population dynamics and gene flow. In white-tailed deer (WTD; Odocoileus virginianus), dispersal also presents an increasingly relevant risk for the spread of infectious diseases. Across their wide range, WTD dispersal is believed to be driven by a suite of landscape and host behavioral factors, but these can vary by region, season, and sex. Our objectives were to (1) identify dispersal events in Wisconsin WTD and determine drivers of dispersal rates and distances, and (2) determine how landscape features (e.g., rivers, roads) structure deer dispersal paths.

METHODS

We developed an algorithmic approach to detect dispersal events from GPS collar data for 590 juvenile, yearling, and adult WTD. We used statistical models to identify host and landscape drivers of dispersal rates and distances, including the role of agricultural land use, the traversability of the landscape, and potential interactions between deer. We then performed a step selection analysis to determine how landscape features such as agricultural land use, elevation, rivers, and roads affected deer dispersal paths.

RESULTS

Dispersal predominantly occurred in juvenile males, of which 64.2% dispersed, with dispersal events uncommon in other sex and age classes. Juvenile male dispersal probability was positively associated with the proportion of the natal range that was classified as agricultural land use, but only during the spring. Dispersal distances were typically short (median 5.77 km, range: 1.3-68.3 km), especially in the fall. Further, dispersal distances were positively associated with agricultural land use in potential dispersal paths but negatively associated with the number of proximate deer in the natal range. Lastly, we found that, during dispersal, juvenile males typically avoided agricultural land use but selected for areas near rivers and streams.

CONCLUSION

Land use-particularly agricultural-was a key driver of dispersal rates, distances, and paths in Wisconsin WTD. In addition, our results support the importance of deer social environments in shaping dispersal behavior. Our findings reinforce knowledge of dispersal ecology in WTD and how landscape factors-including major rivers, roads, and land-use patterns-structure host gene flow and potential pathogen transmission.

CAUSE OF DEATH, PATHOLOGY, AND CHRONIC WASTING DISEASE STATUS OF WHITE-TAILED DEER (ODOCOILEUS VIRGINIANUS) MORTALITIES IN WISCONSIN, USA

White-tailed deer (WTD; Odocoileus virginianus) are a critical species for ecosystem function and wildlife management. As such, studies of cause-specific mortality among WTD have long been used to understand population dynamics. However, detailed pathological information is rarely documented for free-ranging WTD, especially in regions with a high prevalence of chronic wasting disease (CWD). This leaves a significant gap in understanding how CWD is associated with disease processes or comorbidities that may subsequently alter broader population dynamics. We investigated unknown mortalities among collared WTD in southwestern Wisconsin, USA, an area of high CWD prevalence. We tested for associations between CWD and other disease processes and used a network approach to test for co-occurring disease processes. Predation and infectious disease were leading suspected causes of death, with high prevalence of CWD (42.4%; of 245 evaluated) and pneumonia (51.2%; of 168 evaluated) in our sample. CWD prevalence increased with age, before decreasing among older individuals, with more older females than males in our sample. Females were more likely to be CWD positive, and although this was not statistically significant when accounting for age, females were significantly more likely to die with end-stage CWD than males and may consequently be an underrecognized source of CWD transmission. Presence of CWD was associated with emaciation, atrophy of marrow fat and hematopoietic cells, and ectoparasitism (lice and ticks). Occurrences of severe infectious disease processes clustered together (e.g., pneumonia, CWD), as compared to noninfectious or low-severity processes (e.g., sarcocystosis), although pneumonia cases were not fully explained by CWD status. With the prevalence of CWD increasing across North America, our results highlight the critical importance of understanding the potential role of CWD in favoring or maintaining disease processes of importance for deer population health and dynamics.

Accuracies and biases of ageing white-tailed deer in semiarid environments

Abstract Context The ability to accurately estimate age of animals is important for both research and management. The two methods for age estimation in ungulates are tooth replacement and wear (TRW) and cementum annuli (CA). Errors in estimated TRW ages are commonly attributed to environmental conditions; however, the influence of environmental variables on tooth wear has not been quantified. Further, the performance of CA in environments with weak seasonality has not been thoroughly evaluated. Aims The study had the following three goals: identify environmental and morphological factors that influenced estimated ages, quantify accuracy of TRW and CA, and develop TRW ageing criteria that minimise error. Methods We used data from harvested (n = 5117) and free-ranging, known-age white-tailed deer (n = 134) collected in southern Texas, USA, to quantify environmental and morphological influences on estimated TRW ages, and assess biases in both methods. Key results We observed substantial variation in age estimates for both TRW and CA. Soil, drought and supplemental nutrition had minor effects on tooth wear, insufficient to alter age estimates by ≥1 year. Body mass and antler size influenced age estimates for TRW only for extreme outliers. Both methods were biased and tended to under-estimate ages of adult deer, especially TRW. Wear on the first molar was most correlated with the known age (r2 = 0.78) and allowed biologists to correctly place known-age deer into age classes of 2, 3–5, and ≥6 years old 72%, 73% and 68% of the time, an improvement compared with the 79%, 48% and 28% accuracy from pooled TRW. Conclusions We observed substantial inter- and intra-individual variation in tooth-wear patterns that became more pronounced in older deer. Individual variation had a greater influence on TRW ages than did environmental covariates, whereas CA ages appeared unaffected by environment. Although variable, age estimates were ±1 year of the true age 87% and 93% of the time for TRW and CA respectively. Implications Managers, ecologists and epidemiologists often incorporate ages into population models. The high inter-individual variation in estimated ages, the tendency to underestimate ages of older deer, and the ageing method need to be considered.

Age structuring and spatial heterogeneity in prion protein gene (PRNP) polymorphism in white-tailed deer

Chronic-wasting disease (CWD) is a prion-derived fatal neurodegenerative disease that has affected wild cervid populations on a global scale. Susceptibility has been linked unambiguously to several amino acid variants within the prion protein gene (PRNP). Quantifying their distribution across landscapes can provide critical information for agencies attempting to adaptively manage CWD. Here we attempt to further define management implications of PRNP polymorphism by quantifying the contemporary geographic distribution (i.e., phylogeography) of PRNP variants in hunter-harvested white-tailed deer (WTD; Odocoileus virginianus, N = 1433) distributed across Arkansas (USA), including a focal spot for CWD since detection of the disease in February 2016. Of these, PRNP variants associated with the well-characterized 96S non-synonymous substitution showed a significant increase in relative frequency among older CWD-positive cohorts. We interpreted this pattern as reflective of a longer life expectancy for 96S genotypes in a CWD-endemic region, suggesting either decreased probabilities of infection or reduced disease progression. Other variants showing statistical signatures of potential increased susceptibility, however, seemingly reflect an artefact of population structure. We also showed marked heterogeneity across the landscape in the prevalence of ‘reduced susceptibility’ genotypes. This may indicate, in turn, that differences in disease susceptibility among WTD in Arkansas are an innate, population-level characteristic that is detectable through phylogeographic analysis.

Spatial variation in antler investment of Apennine red deer

Heterogeneity in resource availability and quality can trigger spatial patterns in the expression of sexually selected traits such as body mass and weaponry. While relationships between habitat features and phenotypic quality are well established at broad geographical scales, information is poor on spatial patterns at finer, intrapopulation scales. We analyzed biometric data collected on 1965 red deer Cervus elaphus males over 20 years from a nonmigratory population living on two sides of a mountainous ridge, with substantial differences in land cover and habitat quality but similar climate and population density. We investigate spatial patterns in (i) body mass, (ii) antler mass, and (iii) antler investment. We also tested for site- and age-specific patterns in allometric relationship between body mass and antler mass. Statistically significant fine-scale spatial variations in body mass, antler mass, and, to a lesser extent, antler allocation matched spatial differences in land cover. All three traits were greater in the northern slope, characterized by higher habitat heterogeneity and greater availability of open habitats, than in the southern slope. Moreover, the allometric relationship between body mass and antler mass differed among age-classes, in a pattern that was consistent between the two mountain slopes. Our results support the occurrence of spatial patterns in the expression of individual attributes also at a fine, intrapopulation scale. Our findings emphasize the role of environmental heterogeneity in shaping spatial variations of key life-history traits, with potential consequences for reproductive success.

Weaning, parturitions and illnesses are recorded in rhesus macaque (Macaca mulatta) dental cementum microstructure

Many open questions in evolutionary studies relate to species' physiological adaptations, including the evolution of their life history and reproductive strategies. There are few empirical methods capable of detecting and timing physiologically impactful events such as weaning, parturition and illnesses from hard tissue remains of either extant or extinct species. Cementum is an incremental tissue with post eruption annual periodicity, which covers the tooth root and functions as a recording structure of an animal's physiology. Here we test the hypothesis that it is possible to detect and time physiologically impactful events through the analysis of dental cementum microstructure. Our sample comprises 41 permanent and deciduous teeth from male and female rhesus macaques (Macaca mulatta) with known medical, lifestyle and life history information. We develop a semi-automated method of cementum histological analysis for the purpose of event detection and timing, aimed at significantly reducing the amount of intra- and interobserver errors typically associated with histological analyses. The results of our work show that we were able to detect known events including weaning, parturition, illness and physical trauma with high accuracy (false negative rate = 3.2%; n = 1), and to time them within an average absolute difference of 0.43 years (R²  = .98; p < .05). Nonetheless, we could not distinguish between the several types of stressful events underlying the changes in cementum microstructure. While this study is the first to identify a variety of life history events in macaque dental cementum, laying foundations for future work in conservation and evolutionary studies of both primates and toothed mammals at large, there are some limitations. Other types of analyses (possibly chemical ones) are necessary to tease apart the causes of the stressors.

Male size and alternative mating tactics in white-tailed deer and mule deer

Within populations, individual males adopt different courtship tactics due to differences in their competitive ability, which may vary depending on the animal’s age and size. To test the hypothesis that mule deer (Odocoileus hemionus) and white-tailed deer (O. virginianus) males vary their courtship behavior based on their size, we conducted focal observations of 144 mule deer and 85 white-tailed males that varied in size, at a large grassland site in southern Alberta. The smallest mule deer males devoted more time to feeding, were less likely to engage in late-stage courtship than larger males and were less likely to move among female groups. Other males, including small white-tailed males, appeared to use a roving strategy to search for estrous females in different groups, which is consistent with recent research on male movements. Both medium and large males increased the time they spent in one-male groups, and specifically isolated pairs, as courtship advanced, presumably to reduce competition with other males. However, this trend was most pronounced for medium mule deer males, and for all size classes of white-tailed deer. In contrast, large mule deer males spent a similar proportion of time tending females in all group types. Our results identified potential size-dependent tactics for mule deer males. In contrast, white-tailed males of all sizes appeared to rely on a tactic of finding and tending estrous females in isolation from other males.

Precision of cementum annuli method for aging male white-tailed deer

The most common method used to estimate ages of harvested white-tailed deer (Odocoileus virginianus) and other cervids is a criterion based on tooth replacement-and-wear (TRW). Previous studies have shown this method is prone to considerable error because TRW is partially subjective. A presumably more accurate, but more labor intensive and expensive, method to estimate age involves the counting of cementum annuli (CA) of cross-sectioned incisors. Quantifying rate of error of the CA aging method is not possible without known-aged specimens, but precision of duplicate CA age estimates for two teeth may be related to accuracy if identical factors influence both CA accuracy and precision. The objective of this research was to identify and assess factors affecting precision of paired CA ages as well as evaluate congruence between TRW and CA age estimates. We obtained paired CA age estimates from a laboratory specializing in CA aging for 473 adult (≥ 1 year old), male white-tailed deer harvested in Iowa (USA; 2014–2018). Not all CA age estimates of paired incisors agreed with one another and probability of agreement between the paired CA ages decreased as the certainty level of the CA ages provided by the laboratory decreased and was dependent upon the batches in which they were aged by the laboratory. We also estimated the age of 1,292 adult, male deer using both TRW and CA methods and compared the congruence between the TRW and CA age estimates. Congruence rates of CA and TRW ages differed among age classes (80% congruence in yearling TRW age classification, 65% with 2-year-olds, 78% with ≥3-year-olds). Our results showed that CA aging is imperfect and that the certainty level is an important factor to consider with CA ages, as shown in previous research, as is the batch in which the teeth were aged. We also confirmed previous studies’ findings that CA and TRW ages for adult deer are not always congruent, particularly in age classes other than the yearling age class. Our results suggest managers are best served by using TRW to age adult deer as yearlings or ≥2-years-old. If additional age classes are required, CA aging is likely to be a better tool than TRW.

Estimating body mass of Florida white-tailed deer from standard age and morphometric measurements

Context Measuring a mammal’s body mass has importance in understanding nutritional condition, reproductive biology and ecology. It can be impractical for a researcher to measure the body mass when equipment needed to weigh individuals is inadequate or unavailable. Aims The purpose of this study was to develop a model to accurately estimate the body mass of hunter-harvested Florida white-tailed deer (Odocoileus virginianus osceola, Odocoileus virginianus seminolus) based on the relationship between scale mass, sex and standard age and morphometric measurement predictor variables easily obtainable in the field. Methods An information-theoretic approach was used to evaluate simple and multiple linear regression models with 67% of the data, and the best model in the set was validated using the remaining 33%. Key results Chest girth was the best single predictor of body mass. A global model including sex, age, age2 and body length variables was better supported than chest girth alone, and subspecies information did not contribute significantly to the body-mass–predictor-variable relationship. The best model explained 98.5% of the variation in body mass as follows: body mass (kg) = –18.41 + 6.53 × sex (0 = female, 1 = male) + 5.04 × age (year) – 0.49 × age2 (year2) + 4.76 × 10−3 × chest girth2 (cm2) + 0.12 × body length (cm). The 95% confidence interval on the bias of the estimated body mass of the best model was –0.50 to 0.59 kg. The difference between estimated and scale body mass was –0.04 kg ± 0.28 (s.e.). Conclusions Individuals maintained a similar proportion of body mass to predictor variables, and differences between the observed and estimated body mass of model applied to the validation dataset were not significant. Implications The validated body-mass-estimation model presented will enable accurate estimates of the body mass of white-tailed deer in cases where standard age and morphometric measurements are available, but the individuals were not weighed. These results provide a basis to formulate and parameterise body-mass-estimation models for other white-tailed deer subspecies and populations. Without the need for specialised equipment, the body-mass-estimation model can be used by personnel involved in white-tailed deer research, management and sport hunting to assess trends in individual and population health in support of this species’ conservation. Photograph by Carlton Ward Jr.

Chronic wasting disease in white-tailed deer: infection, mortality, and implications for heterogeneous transmission

Chronic wasting disease (CWD) is a fatal neurodegenerative disease affecting free-ranging and captive cervids that now occurs in 24 U.S. states and two Canadian provinces. Despite the potential threat of CWD to deer populations, little is known about the rates of infection and mortality caused by this disease. We used epidemiological models to estimate the force of infection and disease-associated mortality for white-tailed deer in the Wisconsin and Illinois CWD outbreaks. Models were based on age-prevalence data corrected for bias in aging deer using the tooth wear and replacement method. Both male and female deer in the Illinois outbreak had higher corrected age-specific prevalence with slightly higher female infection than deer in the Wisconsin outbreak. Corrected ages produced more complex models with different infection and mortality parameters than those based on apparent prevalence. We found that adult male deer have a more than threefold higher risk of CWD infection than female deer. Males also had higher disease mortality than female deer. As a result, CWD prevalence was twofold higher in adult males than females. We also evaluated the potential impacts of alternative contact structures on transmission dynamics in Wisconsin deer. Results suggested that transmission of CWD among male deer during the nonbreeding season may be a potential mechanism for producing higher rates of infection and prevalence characteristically found in males. However, alternatives based on high environmental transmission and transmission from females to males during the breeding season may also play a role.