Tracking the fecal mycobiome through the lifespan of production pigs and a comparison to the feral pig.

IMPORTANCE: This work provides evidence that early-life fungal community composition, or host genetics, influences long-term mycobiome composition. In addition, this work provides the first comparison of the feral pig mycobiome to the mycobiome of intensively raised pigs.

Correction: Publication reform to safeguard wildlife from researcher harm.

[This corrects the article DOI: 10.1371/journal.pbio.3000193.].

Publication reform to safeguard wildlife from researcher harm.

Despite abundant focus on responsible care of laboratory animals, we argue that inattention to the maltreatment of wildlife constitutes an ethical blind spot in contemporary animal research. We begin by reviewing significant shortcomings in legal and institutional oversight, arguing for the relatively rapid and transformational potential of editorial oversight at journals in preventing harm to vertebrates studied in the field and outside the direct supervision of institutions. Straightforward changes to animal care policies in journals, which our analysis of 206 journals suggests are either absent (34%), weak, incoherent, or neglected by researchers, could provide a practical, effective, and rapidly imposed safeguard against unnecessary suffering. The Animals in Research: Reporting On Wildlife (ARROW) guidelines we propose here, coupled with strong enforcement, could result in significant changes to how animals involved in wildlife research are treated. The research process would also benefit. Sound science requires animal subjects to be physically, physiologically, and behaviorally unharmed. Accordingly, publication of methods that contravenes animal welfare principles risks perpetuating inhumane approaches and bad science.

Predicting functional responses in agro-ecosystems from animal movement data to improve management of invasive pests.

Functional responses describe how changing resource availability affects consumer resource use, thus providing a mechanistic approach to prediction of the invasibility and potential damage of invasive alien species (IAS). However, functional responses can be context dependent, varying with resource characteristics and availability, consumer attributes, and environmental variables. Identifying context dependencies can allow invasion and damage risk to be predicted across different ecoregions. Understanding how ecological factors shape the functional response in agro-ecosystems can improve predictions of hotspots of highest impact and inform strategies to mitigate damage across locations with varying crop types and availability. We linked heterogeneous movement data across different agro-ecosystems to predict ecologically driven variability in the functional responses. We applied our approach to wild pigs (Sus scrofa), one of the most successful and detrimental IAS worldwide where agricultural resource depredation is an important driver of spread and establishment. We used continental-scale movement data within agro-ecosystems to quantify the functional response of agricultural resources relative to availability of crops and natural forage. We hypothesized that wild pigs would selectively use crops more often when natural forage resources were low. We also examined how individual attributes such as sex, crop type, and resource stimulus such as distance to crops altered the magnitude of the functional response. There was a strong agricultural functional response where crop use was an accelerating function of crop availability at low density (Type III) and was highly context dependent. As hypothesized, there was a reduced response of crop use with increasing crop availability when non-agricultural resources were more available, emphasizing that crop damage levels are likely to be highly heterogeneous depending on surrounding natural resources and temporal availability of crops. We found significant effects of crop type and sex, with males spending 20% more time and visiting crops 58% more often than females, and both sexes showing different functional responses depending on crop type. Our application demonstrates how commonly collected animal movement data can be used to understand context dependencies in resource use to improve our understanding of pest foraging behavior, with implications for prioritizing spatiotemporal hotspots of potential economic loss in agro-ecosystems.

Density-dependent habitat selection and partitioning between two sympatric ungulates.

Theory on density-dependent habitat selection predicts that as population density of a species increases, use of higher quality (primary) habitat by individuals declines while use of lower quality (secondary) habitat rises. Habitat partitioning is often considered the primary mechanism for coexistence between similar species, but how this process evolves with changes in population density remains to be empirically tested for free-ranging ungulates. We used resource-selection functions to quantify density effects on landscape-scale habitat selection of two sympatric species of ungulates [moose (Alces alces) and elk (Cervus canadensis manitobensis)] in Riding Mountain National Park, Manitoba, Canada (2000-2011). The density of elk was actively reduced from 1.2 to 0.4 elk km(-2) through increased hunting effort during the period of study, while moose density decreased without additional human influence from 1.6-0.7 moose km(-2). Patterns of habitat selection during winter by both species changed in accordance to expectations from density-dependent habitat-selection theory. At low intraspecific density, moose and elk did not partition habitat, as both species selected strongly for mixed forest (primary habitat providing both food and cover), but did so in different areas segregated across an elevational gradient. As intraspecific density increased, selection for primary habitat by both species decreased, while selection for secondary, lower quality habitat such as agricultural fields (for elk) and built-up areas (for moose) increased. We show that habitat-selection strategies during winter for moose and elk, and subsequent effects on habitat partitioning, depend heavily on the position in state space (density) of both species.

Unregulated Online Sales are High-Risk Sources of Domestic Swine (Sus scrofa) in Canada: Implications for Invasive Wild Pig and AfricanSwine Fever Risk Preparedness.

Free-ranging wild pig (Sus scrofa) populations may cause widespread environmental damage and transmit diseases at the wildlife-livestock interface. For example, African swine fever (ASF) is a highly contagious viral disease of pigs capable of causing catastrophic economic losses. Prevention and preparedness for ASF require understanding wild and domestic pig movements and distribution. We characterized a "grey" swine market and described the risks it poses, contributing to the threats associated with wild pig populations. We monitored www.kijiji.ca, a Canadian internet classified advertising service, for sales of domestic wild boar, pot-bellied pigs, other breeds, and their hybrids across Canada from 28 April to 30 June 2021. Data collected included seller-defined breed, age, sex, number for sale, sexual intactness, presence of identifying tags or tattoos, and the date and location of listings. Advertisement locations were mapped and compared with existing wild pig distributions, identifying areas new populations might be established, and existing populations supplemented or genetically diversified. We identified 151 advertisements on Kijiji: 34% (n=52/151) from Ontario, 29% (n=44/151) from Alberta, 41% (n=62/151) from existing wild pig populations, and 59% (n=89/151) from areas where wild pigs have not yet been identified. We propose requiring the use of individual animal identifiers (tags/tattoos), genetic analysis, and mandatory reporting for all pig sales in Canada to aid in ASF preparedness and to increase regulation and enforcement of the online swine market.

Landscape resistance to dispersal: simulating long-term effects of human disturbance on a small and isolated wolf population in southwestern Manitoba, Canada.

Landscape fragmentation affects wildlife population viability, in part, through the effects it has on individual dispersal. In addition, some forms of human disturbance impinge on dispersal without physically fragmenting habitats. Here, we use the term "landscape resistance" to capture constraints to dispersal that cannot be linked directly to fragmentation. The extent to which landscape resistance can influence population persistence is not well understood. Agricultural development over the past 60 years has resulted in considerable habitat fragmentation in the Riding Mountain National Park (RMNP) region in southwestern Manitoba, Canada. We examined how park boundaries, roads outside park boundaries and negative human attitudes have altered dispersal success and population persistence. We examined whether stochastic disturbance, representing infectious disease epidemics, further reduced long-term population persistence for various scenarios. Finally, we assessed whether the simultaneous occurrence of the three features had additive effects. We simulated dispersal using HexSim, a spatially explicit individual-based population model, parameterised with data on wolves (Canis lupus) in the RMNP region. Simulations that separately accounted for negative human attitudes and roads outside the park boundaries exhibited lower mean population size than those that ignored these details. Increasing deflection from park boundaries did not appear to have significant impacts. Our results did not indicate the presence of additive effects, and scenarios incorporating all three features had similar results as that of roads. Stochastic disturbance further reduced mean population size. Our results do illustrate how less-visible human disturbances (i.e. those that do not clearly alter landscape characteristics) can significantly limit dispersal and population persistence.

Enhancing inter-organizational collaboration for wildlife disease surveillance in Sri Lanka.

Management of zoonotic infectious diseases is an urgent global heath imperative. Interdisciplinary approaches for zoonosis management exist in literature, but collaboratively implementing them is a pervasive challenge. The Sri Lanka Wildlife Health Centre (SLWHC) was created in 2011 to coordinate wildlife disease surveillance and response among government agencies. We interviewed SLWHC-affiliated personnel about existing communication and collaboration channels to identify operational needs as well as potential enhancements for the SLWHC's operations. We used the Policy Sciences' analytical framework to identify opportunities and challenges for the SLWHC. Study participants held both human and animal health as the utmost priorities. However, their observations indicate that inter-organizational communication barriers and intra-organizational hierarchies still need to be overcome for the Centre's partnering organizations to collaborate to their fullest potential. Any interventions to enhance the SLWHC's collaborative capacity for detecting and managing zoonotic disease outbreaks could be strengthened by appealing to participants' shared value orientations towards enlightenment and respect. A common interest was the desire to collaborate and combine resources, knowledge and personnel to detect, reduce and prevent the incidence of zoonotic disease outbreaks in Sri Lanka. These lessons about institutionalizing communication have considerable relevance for organizational responses to the current SARS-CoV2 pandemic and other zoonoses.

Understanding and strengthening wildlife and zoonotic disease policy processes: A research imperative.

The COVID-19 pandemic highlights the urgency and importance of monitoring, managing and addressing zoonotic diseases, and the acute challenges of doing so with sufficient inter-jurisdictional coordination in a dynamic global context. Although wildlife pathogens are well-studied clinically and ecologically, there is very little systematic scholarship on their management or on policy implications. The current global pandemic therefore presents a unique social science research imperative: to understand how decisions are made about preventing and responding to wildlife diseases, especially zoonoses, and how those policy processes can be improved as part of early warning systems, preparedness and rapid response. To meet these challenges, we recommend intensified research efforts towards: (i) generating functional insights about wildlife and zoonotic disease policy processes, (ii) enabling social and organizational learning to mobilize those insights, (iii) understanding epistemic instability to address populist anti-science and (iv) anticipating evolving and new zoonotic emergences, especially their human dimensions. Since policy processes for zoonoses can be acutely challenged during the early stages of an epidemic or pandemic, such insights can provide a pragmatic, empirically-based roadmap for enhancing their robustness and efficacy, and benefiting long-term decision-making efforts.

A pilot study of the impact of bovine spongiform encephalopathy on the futures of rural youth and Canadian farming.

There is an abundance of literature examining the economic impact of Canada's bovine spongiform encephalopathy (BSE) outbreak, but few studies examined the impact of such a crisis on health at the individual, family, or community levels. In particular, rural youth represent an under-researched population despite being at risk for a unique set of social and health concerns. In this pilot study, our objectives were to explore how rural youth responded to Canada's BSE crisis and how they perceived themselves, their families, and their communities to have been impacted. Seven youths (n = 7), recruited from within a university setting using a snowball sampling method, were interviewed. They represent a segment of rural, agriculturally based youth who are resilient due to good parental support. Although they reported high stress in their families during the immediate crisis in 2003, they did not report lasting high levels of stress or negative health effects due to BSE. They did report a decline in rural community health, identifying a reduction in community activities and in the participation of families in community activities. Participants identified elements that discourage youth from pursuing farming as a career and expressed concern for the future of family farming. The results are discussed in terms of the ability of agriculturally based youth to make the transition to adulthood. The implications have importance for future research and policy that addresses the structural supports for choice making, the long-term success for rural youth in transitioning to adult status, and the future of agriculture.

Evaluation and delivery of domestic animal health services in remote communities in the Northwest Territories: A case study of status and needs.

Domestic animal health services are supplied to communities in Canada's Northwest Territories (NT) in diverse ways, including private veterinary practices in 2 of 33 communities, and by mail-order, fly-in, free clinics, and a government-coordinated lay vaccinator program in some of the other 31 communities. We evaluated delivery, needs, and potential uptake of domestic animal health services in the Sahtu Settlement Area, NT by offering free clinics for 225 dogs in 2008 and 2009; and administered questionnaires to 42 dog owners and 67 students in 2008. Owners indicated that 20% of dogs were neutered, 37% had had rabies vaccinations, and 29% had been dewormed. Physical examination of dogs demonstrated that 54% were "thin" and 4% were "emaciated." Owners and youth showed a range of attitudes toward dogs and supported improved domestic animal health services. Future services need to build on existing programs and collaborate with communities to ensure relevance, ownership, and sustainability.

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2.

Motion-activated wildlife cameras (or "camera traps") are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the "species model," and one that determines if an image is empty or if it contains an animal, the "empty-animal model." Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%-91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%-94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.

Evaluating Cost-Effective Methods for Rapid and Repeatable National Scale Detection and Mapping of Invasive Species Spread.

Invasive species can spread rapidly at local and national scales, creating significant environmental and economic impacts. A central problem in mitigation efforts is identifying methods that can rapidly detect invasive species in a cost-effective and repeatable manner. This challenge is particularly acute for species that can spread over large areas (>1 million km2). Wild pigs (Sus scrofa) are one of the most prolific invasive mammals on Earth and cause extensive damage to agricultural crops, native ecosystems, and livestock, and are reservoirs of disease. They have spread from their native range in Eurasia and North Africa into large areas of Australia, Africa, South America, and North America. We show that the range of invasive wild pigs has increased exponentially in Canada over the last 27 years following initial and ongoing releases and escapes from domestic wild boar farms. The cumulative range of wild pigs across Canada is 777,783 km2, with the majority of wild pig distribution occurring in the Prairie Provinces. We evaluate eight different data collection and evaluation/validation methods for mapping invasive species over large areas, and assess their benefits and limitations. Our findings effectively map the spread of a highly invasive large mammal and demonstrate that management efforts should ideally rely on a set of complementary independent monitoring methods. Mapping and evaluating resulting species occurrences provide baseline maps against which future changes can be rapidly evaluated.

Spatio-temporal trends in crop damage inform recent climate-mediated expansion of a large boreal herbivore into an agro-ecosystem.

Large-scale climatic fluctuations have caused species range shifts. Moose (Alces alces) have expanded their range southward into agricultural areas previously not considered moose habitat. We found that moose expansion into agro-ecosystems is mediated by broad-scale climatic factors and access to high-quality forage (i.e., crops). We used crop damage records to quantify moose presence across the Canadian Prairies. We regressed latitude of crop damage against North Atlantic Oscillation (NAO) and crop area to test the hypotheses that NAO-mediated wetland recharge and occurrence of more nutritious crop types would result in more frequent occurrences of crop damage by moose at southerly latitudes. We examined local-scale land use by generating a habitat selection model to test our hypothesis that moose selected for areas of high crop cover in agro-ecosystems. We found that crop damage by moose occurred farther south during dry winters and in years with greater coverage of oilseeds. The results of our analyses support our hypothesis that moose movement into cropland is mediated by high-protein crops, but not by thermoregulatory habitat at the scale examined. We conclude that broad-scale climate combined with changing land-use regimes are causal factors in species' range shifts and are important considerations when studying changing animal distributions.

Fencing Large Predator-Free and Competitor-Free Landscapes for the Recovery of Woodland Caribou in Western Alberta: An Ineffective Conservation Option.

n/a.

Intranasal administration of xylazine to reduce stress in elk captured by net gun.

Forty free-ranging elk (Cervus elaphus manitobensis) were captured by net gun in Riding Mountain National Park (Manitoba, Canada) during February 2002 and were administered either saline (control) or xylazine by the intranasal route, to evaluate the efficacy and benefit of intranasal xylazine to reduce stress. Elk that received xylazine had higher relaxation scores than control elk, and the onset of sedation occurred quickly, often <1 min. Serum concentrations of cortisol, creatine kinase, and gamma-glutamyltransferase were lower in elk that received xylazine than in control elk. At the conclusion of handling, the intravenous administration of yohimbine quickly abolished the sedative effect of xylazine, which allowed elk to be released without concern of physical injury due to ataxia. The intranasal administration of xylazine can be used to reduce stress in wild animals under situations where they are being handled while physically restrained.

Impacts of wildlife baiting and supplemental feeding on infectious disease transmission risk: a synthesis of knowledge.

Baiting and supplemental feeding of wildlife are widespread, yet highly controversial management practices, with important implications for ecosystems, livestock production, and potentially human health. An often underappreciated threat of such feeding practices is the potential to facilitate intra- and inter-specific disease transmission. We provide a comprehensive review of the scientific evidence of baiting and supplemental feeding on disease transmission risk in wildlife, with an emphasis on large herbivores in North America. While the objectives of supplemental feeding and baiting typically differ, the effects on disease transmission of these practices are largely the same. Both feeding and baiting provide wildlife with natural or non-natural food at specific locations in the environment, which can result in large congregations of individuals and species in a small area and increased local densities. Feeding can lead to increased potential for disease transmission either directly (via direct animal contact) or indirectly (via feed functioning as a fomite, spreading disease into the adjacent environment and to other animals). We identified numerous diseases that currently pose a significant concern to the health of individuals and species of large wild mammals across North America, the spread of which are either clearly facilitated or most likely facilitated by the application of supplemental feeding or baiting. Wildlife diseases also have important threats to human and livestock health. Although the risk of intra- and inter-species disease transmission likely increases when animals concentrate at feeding stations, only in a few cases was disease prevalence and transmission measured and compared between populations. Mostly these were experimental situations under controlled conditions, limiting direct scientific evidence that feeding practices exacerbates disease occurrence, exposure, transmission, and spread in the environment. Vaccination programs utilizing baits have received variable levels of success. Although important gaps in the scientific literature exist, current information is sufficient to conclude that providing food to wildlife through supplemental feeding or baiting has great potential to negatively impact species health and represents a non-natural arena for disease transmission and preservation. Ultimately, this undermines the initial purpose of feeding practices and represents a serious risk to the maintenance of biodiversity, ecosystem functioning, human health, and livestock production. Managers should consider disease transmission as a real and serious concern in their decision to implement or eliminate feeding programs. Disease surveillance should be a crucial element within the long-term monitoring of any feeding program in combination with other available preventive measures to limit disease transmission and spread.

Density-dependent effects on group size are sex-specific in a gregarious ungulate.

Density dependence can have marked effects on social behaviors such as group size. We tested whether changes in population density of a large herbivore (elk, Cervus canadensis) affected sex-specific group size and whether the response was density- or frequency-dependent. We quantified the probability and strength of changes in group sizes and dispersion as population density changed for each sex. We used group size data from a population of elk in Manitoba, Canada, that was experimentally reduced from 1.20 to 0.67 elk/km(2) between 2002 and 2009. Our results indicated that functional responses of group size to population density are sex-specific. Females showed a positive density-dependent response in group size at population densities ≥0.70 elk/km(2) and we found evidence for a minimum group size at population density ≤0.70 elk/km(2). Changes in male group size were also density-dependent; however, the strength of the relationship was lower than for females. Density dependence in male group size was predominantly a result of fusion of solitary males into larger groups, rather than fusion among existing groups. Our study revealed that density affects group size of a large herbivore differently between males and females, which has important implications for the benefits e.g., alleviating predation risk, and costs of social behaviors e.g., competition for resources and mates, and intra-specific pathogen transmission.