DNA left on browsed twigs uncovers bite-scale resource use patterns in European ungulates

Facing the facts: adaptive trade-offs along body size ranges determine mammalian craniofacial scaling

The mammalian cranium (skull without lower jaw) is representative of mammalian diversity and is thus of particular interest to mammalian biologists across disciplines. One widely retrieved pattern accompanying mammalian cranial diversification is referred to as 'craniofacial evolutionary allometry' (CREA). This posits that adults of larger species, in a group of closely related mammals, tend to have relatively longer faces and smaller braincases. However, no process has been officially suggested to explain this pattern, there are many apparent exceptions, and its predictions potentially conflict with well-established biomechanical principles. Understanding the mechanisms behind CREA and causes for deviations from the pattern therefore has tremendous potential to explain allometry and diversification of the mammalian cranium. Here, we propose an amended framework to characterise the CREA pattern more clearly, in that 'longer faces' can arise through several kinds of evolutionary change, including elongation of the rostrum, retraction of the jaw muscles, or a more narrow or shallow skull, which all result in a generalised gracilisation of the facial skeleton with increased size. We define a standardised workflow to test for the presence of the pattern, using allometric shape predictions derived from geometric morphometrics analysis, and apply this to 22 mammalian families including marsupials, rabbits, rodents, bats, carnivores, antelopes, and whales. Our results show that increasing facial gracility with size is common, but not necessarily as ubiquitous as previously suggested. To address the mechanistic basis for this variation, we then review cranial adaptations for harder biting. These dictate that a more gracile cranium in larger species must represent a structural sacrifice in the ability to produce or withstand harder bites, relative to size. This leads us to propose that facial gracilisation in larger species is often a product of bite force allometry and phylogenetic niche conservatism, where more closely related species tend to exhibit more similar feeding ecology and biting behaviours and, therefore, absolute (size-independent) bite force requirements. Since larger species can produce the same absolute bite forces as smaller species with less effort, we propose that relaxed bite force demands can permit facial gracility in response to bone optimisation and alternative selection pressures. Thus, mammalian facial scaling represents an adaptive by-product of the shifting importance of selective pressures occurring with increased size. A reverse pattern of facial 'shortening' can accordingly also be found, and is retrieved in several cases here, where larger species incorporate novel feeding behaviours involving greater bite forces. We discuss multiple exceptions to a bite force-mediated influence on facial proportions across mammals which lead us to argue that ecomorphological specialisation of the cranium is likely to be the primary driver of facial scaling patterns, with some developmental constraints as possible secondary factors. A potential for larger species to have a wider range of cranial functions when less constrained by bite force demands might also explain why selection for larger sizes seems to be prevalent in some mammalian clades. The interplay between adaptation and constraint across size ranges thus presents an interesting consideration for a mechanistically grounded investigation of mammalian cranial allometry.

Unraveling the potential of environmental DNA for deciphering recent advances in plant-animal interactions: a systematic review

MAIN CONCLUSION

Environmental DNA-based monitoring provides critical insights for enhancing our understanding of plant-animal interactions in the context of worldwide biodiversity decrease for developing a global framework for effective plant biodiversity conservation. To understand the ecology and evolutionary patterns of plant-animal interactions (PAI) and their pivotal roles in ecosystem functioning advances in molecular ecology tools such as Environmental DNA (eDNA) provide unprecedented research avenues. These methods being non-destructive in comparison to traditional biodiversity monitoring methods, enhance the discernment of ecosystem health, integrity, and complex interactions. This review intends to offer a systematic and critical appraisal of the prospective of eDNA for investigating PAI. The review thoroughly discusses and analyzes the recent reports (2015-2022) employing preferred reporting items for systematic reviews and meta-analyses (PRISMA) to outline the recent progression in eDNA approaches for elucidating PAI. The current review envisages that eDNA has a significant potential to monitor both plants and associated cohort of prospective pollinators (avian species and flowering plants, bees and plants, arthropods and plants, bats and plants, etc.). Furthermore, a brief description of the factors that influence the utility and interpretation of PAI eDNA is also presented. The review establishes that factors such as biotic and abiotic, primer selection and taxonomic resolution, and indeterminate spatio-temporal scales impact the availability and longevity of eDNA. The study also identified the limitations that influence PAI detection and suggested possible solutions for better execution of these molecular approaches. Overcoming these research caveats will augment the assortment of PAI analysis through eDNA that could be vital for ecosystem health and integrity. This review forms a critical guide and offers prominent insights for ecologists, environmental managers and researchers to assess and evaluate plant-animal interaction through environmental DNA.

Drone-assisted collection of environmental DNA from tree branches for biodiversity monitoring

The protection and restoration of the biosphere is crucial for human resilience and well-being, but the scarcity of data on the status and distribution of biodiversity puts these efforts at risk. DNA released into the environment by organisms, i.e., environmental DNA (eDNA), can be used to monitor biodiversity in a scalable manner if equipped with the appropriate tool. However, the collection of eDNA in terrestrial environments remains a challenge because of the many potential surfaces and sources that need to be surveyed and their limited accessibility. Here, we propose to survey biodiversity by sampling eDNA on the outer branches of tree canopies with an aerial robot. The drone combines a force-sensing cage with a haptic-based control strategy to establish and maintain contact with the upper surface of the branches. Surface eDNA is then collected using an adhesive surface integrated in the cage of the drone. We show that the drone can autonomously land on a variety of branches with stiffnesses between 1 and 10³ newton/meter without prior knowledge of their structural stiffness and with robustness to linear and angular misalignments. Validation in the natural environment demonstrates that our method is successful in detecting animal species, including arthropods and vertebrates. Combining robotics with eDNA sampling from a variety of unreachable aboveground substrates can offer a solution for broad-scale monitoring of biodiversity.

Ungulates and Their Impact on Reptiles: A Review of Interspecific Relationships

Several ungulate species are showing increasing population patterns within their geographical distribution ranges, leading to constant interactions with other animal species. Varying densities and activities of different ungulates may result in diverse impacts on other coexisting species groups, including large numbers of threatened species, such as reptiles. In this study, we performed an analysis of the available literature to investigate the impacts of ungulates on reptiles. We aimed to reveal the diversity of: (1) the geographical and environmental distribution of related investigations; (2) the ungulate and reptile species involved; and (3) the characteristics of interactions (direct or indirect, positive or negative) from 69 publications. Our results show that the most papers were reported from the Americas (42%) and Australia (28%). The proportions of studies were balanced for wild ungulates (53%) and livestock (47%). Wild boar (Sus scrofa) was found to be the most problematic species on reptiles whereas reptiles which suffered the harshest impacts were Squamates (i.e., lizards, and snakes). Ungulate activities (e.g., digging by wild boar) may directly harm reptiles (consuming or killing them) or indirectly affect them by modifying their habitats or destroying their hideouts. Some preferential effects were also noted (e.g., by moderate livestock grazing or when wild ungulates are prey for large reptiles). Published livestock impacts were mainly indirect and mostly negatively linked to overgrazing. We conclude that it is important to manage and monitor the densities of ungulates to minimize their negative impacts on reptile species, especially in case of wild boar and grazing livestock, but also to maintain their moderate beneficial effects (e.g., as prey basis).

A molecular method for biomonitoring of an exotic plant-pest: Leafmining for environmental DNA

Understanding how invasive species respond to novel environments is limited by a lack of sensitivity and throughput in conventional biomonitoring methods. Arthropods in particular are often difficult to monitor due to their small size, rapid lifecycles, and/or visual similarities with co-occurring species. This is true for the agromyzid leafminer fly, Liriomyza sativae, a global pest of vegetable and nursery industries that has recently established in Australia. A robust method based on environmental DNA (eDNA) was developed exploiting traces of DNA left inside "empty" leaf mines, which are straightforward to collect and persist longer in the environment than the fly. This extends the window of possible diagnosis to at least 28 days after a leaf mine becomes empty. The test allowed for visually indistinguishable leafmining damage caused by L. sativae to be genetically differentiated from that of other flies. Field application resulted in the identification of new local plant hosts for L. sativae, including widely distributed weeds and common garden crops, which has important implications for the pest's ability to spread. Moreover, the test confirmed the presence of a previously unknown population of L. sativae on an island in the Torres Strait. The developed eDNA method is likely to become an important tool for L. sativae and other leafmining species of biosecurity significance, which, historically, have been difficult to detect, diagnose and monitor. More generally, eDNA is emerging as a highly sensitive and labour-efficient surveillance tool for difficult to survey species to improve outcomes for agricultural industries, global health, and the environment.

Wild ungulate species differ in their contribution to the transmission of Ixodes ricinus-borne pathogens

BACKGROUND

Several ungulate species are feeding and propagation hosts for the tick Ixodes ricinus as well as hosts to a wide range of zoonotic pathogens. Here, we focus on Anaplasma phagocytophilum and Borrelia burgdorferi (s.l.), two important pathogens for which ungulates are amplifying and dilution hosts, respectively. Ungulate management is one of the main tools to mitigate human health risks associated with these tick-borne pathogens. Across Europe, different species of ungulates are expanding their ranges and increasing in numbers. It is currently unclear if and how the relative contribution to the life-cycle of I. ricinus and the transmission cycles of tick-borne pathogens differ among these species. In this study, we aimed to identify these relative contributions for five European ungulate species.

METHODS

We quantified the tick load and collected ticks and spleen samples from hunted fallow deer (Dama dama, n = 131), moose (Alces alces, n = 15), red deer (Cervus elaphus, n = 61), roe deer (Capreolus capreolus, n = 30) and wild boar (Sus scrofa, n = 87) in south-central Sweden. We investigated the presence of tick-borne pathogens in ticks and spleen samples using real-time PCR. We determined if ungulate species differed in tick load (prevalence and intensity) and in infection prevalence in their tissue as well as in the ticks feeding on them.

RESULTS

Wild boar hosted fewer adult female ticks than any of the deer species, indicating that deer are more important as propagation hosts. Among the deer species, moose had the lowest number of female ticks, while there was no difference among the other deer species. Given the low number of infected nymphs, the relative contribution of all ungulate species to the transmission of B. burgdorferi (s.l.) was low. Fallow deer, red deer and roe deer contributed more to the transmission of A. phagocytophilum than wild boar.

CONCLUSIONS

The ungulate species clearly differed in their role as a propagation host and in the transmission of B. burgdorferi and A. phagocytophilum. This study provides crucial information for ungulate management as a tool to mitigate zoonotic disease risk and argues for adapting management approaches to the local ungulate species composition and the pathogen(s) of concern.

Influence of canopy openness, ungulate exclosure, and low-intensity fire for improved oak regeneration in temperate Europe

Failed oak regeneration is widely reported in temperate forests and has been linked in part to changed disturbance regimes and land-use. We investigated if the North American fire-oak hypothesis could be applicable to temperate European oaks (Quercus robur, Quercus petraea) using a replicated field experiment with contrasting canopy openness, protection against ungulate browsing (fencing/no fencing), and low-intensity surface fire (burn/no burn). Survival, relative height growth (RGRH), browsing damage on naturally regenerated oaks (≤300 cm tall), and changes in competing woody vegetation were monitored over three years. Greater light availability in canopy gaps increased oak RGRH (p = .034) and tended to increase survival (p = .092). There was also a trend that protection from browsing positively affected RGRH (p = .058) and survival (p = .059). Burning reduced survival (p < .001), nonetheless, survival rates were relatively high across treatment combinations at the end of the experiment (54%-92%). Most oaks receiving fire were top-killed and survived by producing new sprouts; therefore, RGRH in burned plots became strongly negative the first year. Thereafter, RGRH was greater in burned plots (p = .002). Burning altered the patterns of ungulate browsing frequency on oaks. Overall, browsing frequency was greater during winter; however, in recently burned plots summer browsing was prominent. Burning did not change relative density of oaks, but it had a clear effect on competing woody vegetation as it reduced the number of individuals (p < .001) and their heights (p < .001). Our results suggest that young, temperate European oaks may respond similarly to fire as their North American congeners. However, disturbance from a single low-intensity fire may not be sufficient to ensure a persistent competitive advantage-multiple fires and canopy thinning to increase light availability may be needed. Further research investigating long-term fire effects on oaks of various ages, species-specific response of competitors and implications for biodiversity conservation is needed.

DNA persistence in predator saliva from multiple species and methods for optimal recovery from depredated carcasses

Molecular forensics is an important component of wildlife research and management. Using DNA from noninvasive samples collected at predation sites, we can identify predator species and obtain individual genotypes, improving our understanding of predator–prey dynamics and impacts of predators on livestock and endangered species. To improve sample collection strategies, we tested two sample collection methods and estimated degradation rates of predator DNA on the carcasses of multiple prey species. We fed carcasses of calves (Bos taurus) and lambs (Ovis aires) to three captive predator species: wolves (Canis lupus), coyotes (C. latrans), and mountain lions (Puma concolor). We swabbed the carcass in the field, as well as removed a piece of hide from the carcasses and then swabbed it in the laboratory. We swabbed all tissue samples through time and attempted to identify the predator involved in the depredation using salivary DNA. We found the most successful approach for yielding viable salivary DNA was removing hide from the prey and swabbing it in the laboratory. As expected, genotyping error increased through time and our ability to obtain complete genotypes decreased over time, the latter falling below 50% after 24 h. We provide guidelines for sampling salivary DNA from tissues of depredated carcasses for maximum probability of detection.

Beyond Biodiversity: Can Environmental DNA (eDNA) Cut It as a Population Genetics Tool?

Population genetic data underpin many studies of behavioral, ecological, and evolutionary processes in wild populations and contribute to effective conservation management. However, collecting genetic samples can be challenging when working with endangered, invasive, or cryptic species. Environmental DNA (eDNA) offers a way to sample genetic material non-invasively without requiring visual observation. While eDNA has been trialed extensively as a biodiversity and biosecurity monitoring tool with a strong taxonomic focus, it has yet to be fully explored as a means for obtaining population genetic information. Here, we review current research that employs eDNA approaches for the study of populations. We outline challenges facing eDNA-based population genetic methodologies, and suggest avenues of research for future developments. We advocate that with further optimizations, this emergent field holds great potential as part of the population genetics toolkit.

Environmental DNA from Residual Saliva for Efficient Noninvasive Genetic Monitoring of Brown Bears (Ursus arctos)

Noninvasive genetic sampling is an important tool in wildlife ecology and management, typically relying on hair snaring or scat sampling techniques, but hair snaring is labor and cost intensive, and scats yield relatively low quality DNA. New approaches utilizing environmental DNA (eDNA) may provide supplementary, cost-effective tools for noninvasive genetic sampling. We tested whether eDNA from residual saliva on partially-consumed Pacific salmon (Oncorhynchus spp.) carcasses might yield suitable DNA quality for noninvasive monitoring of brown bears (Ursus arctos). We compared the efficiency of monitoring brown bear populations using both fecal DNA and salivary eDNA collected from partially-consumed salmon carcasses in Southeast Alaska. We swabbed a range of tissue types from 156 partially-consumed salmon carcasses from a midseason run of lakeshore-spawning sockeye (O. nerka) and a late season run of stream-spawning chum (O. keta) salmon in 2014. We also swabbed a total of 272 scats from the same locations. Saliva swabs collected from the braincases of salmon had the best amplification rate, followed by swabs taken from individual bite holes. Saliva collected from salmon carcasses identified unique individuals more quickly and required much less labor to locate than scat samples. Salmon carcass swabbing is a promising method to aid in efficient and affordable monitoring of bear populations, and suggests that the swabbing of food remains or consumed baits from other animals may be an additional cost-effective and valuable tool in the study of the ecology and population biology of many elusive and/or wide-ranging species.

Using eDNA to experimentally test ungulate browsing preferences

Large herbivores may affect ecosystem processes and states, but such effects can be difficult to quantify, especially within multispecies assemblages. To better understand such processes and improve our predictive ability of systems undergoing change, herbivore diets can be studied using controlled feeding trials (or cafeteria tests). With some wildlife, such as large herbivores, it is impractical to empirically verify these findings, because it requires visually observing animals in forested environments, which can disturb them from their natural behaviors. Yet, in field-based cafeteria trials it is nearly impossible to differentiate selection between herbivore species that forage on similar plants and make very similar bite marks. However, during browsing ungulates leave saliva residue which includes some buccal cells and DNA that can be extracted for species identification. Here we used a newly developed eDNA-based method (biteDNA) to test the browsing preferences of four sympatric ungulate species in the wild. Overall, food preferences varied between species, but all species strongly preferred deciduous over coniferous species. Our method allows the study of plant-animal interactions in multispecies assemblages at very fine detail.