Biology subjects

Pepin, K.

Publications and source records attributed to Pepin, K..

11 recordsLinked to original sources

bioRxiv2026

The effect of long-term management on wild pig (Sus scrofa x domesticus) populations across the southeastern United States

O_LIThe management of invasive species often emphasizes removals to manage populations. However, evaluating the success of this management technique remains challenging, especially at large scales. Understanding the relationship between removal intensity and population growth is essential for determining when management achieves desired outcomes. C_LIO_LIWe used management removal data (removal resources [e.g. trapping] and relative effort [trap nights]) to estimate population density, demographic structure, and growth rates of invasive wild pigs (Sus scrofax domesticus) across a large landscape. From the management data and population estimates, we inferred population trajectories in the absence of removals and quantified the proportion of the population removed by the most widely used methods to control wild pigs. We then compared observed removal intensities and population growth rates to predict expected population trajectories immediately after management occurs. C_LIO_LIResults suggest substantial spatial and temporal variation in wild pig growth rates and variation in the effectiveness of removal efforts. Additionally, removing wild pigs at higher densities had a greater effect on limiting population growth than removals conducted at lower densities, though both are important. However, on large properties, removal intensity was often insufficient to offset population growth, indicating that management effort does not scale to large areas. C_LIO_LIThese results demonstrate how removal data and population modeling can provide robust inference on population dynamics and management effectiveness, offering a scalable framework for evaluating and improving invasive species control programs. We also discuss the current limitation of how effort is defined for different large-mammal removal techniques, and offer potential solutions for a more complete definition, such as going beyond trap nights and including constraints on personnel, equipment, and logistics. C_LI

ecology↗

bioRxiv2025

Improving a removal model for evaluating density changes in a widespread invasive species

Invasive species pose a significant threat to native ecosystems. Effective management of invasive species requires accurate abundance estimates through time, particularly at large spatial scales. Traditional methods of abundance estimation from management data, such as camera trap studies and harvest data, face challenges due to variations in sampling protocols and effort standardization. We propose an extension to a previously calibrated removal model by integrating into an Integrated Population Model (IPM) and incorporating multiple removal techniques. The model utilizes management and land cover data, both of which are readily available in many invasive species systems. We evaluate the model with a simulation study, then apply it to management data on wild pigs (Sus scrofa). Simulations showed that the model performs well across a wide range of densities and population trajectories. Density estimates were the most biased when effort and density were low and sharpshooting or fixed wing aircraft were used to conduct removals. We discuss the advantages and limitations of using removal models for invasive species management, how the model performs with respect to previous removal modeling efforts, how performance might be improved through changes to data management practices, and the models potential to inform decision-making processes for invasive species management. Data availabilityThe data for this manuscript is available from Dryad (http://datadryad.org/share/gFz3ClanB-8yPB5lQ1x-dl1JqI07CP3SX92P-9UyfaU). The code for this manuscript will is available from Zenodo (10.5281/zenodo.15784366).

ecology↗

bioRxiv2025

Spatial transmission dynamics of African Swine Fever in wild pigs: Sensitivity to epidemiological traits of different viral strains

African Swine Fever virus (ASFv) is a rapidly spreading animal disease with impacts on global economy and food security. Since the first known case of ASFv in Kenya in 1921, the virus has undergone significant evolution resulting in the emergence of 25 distinct genotypes. These genotypes have a wide variety of epidemiological traits, leading to uncertainty about how a genotype or variant of a genotype might spread in a population. Understanding the impacts of different epidemiological traits on the spread of ASFv is important for developing effective surveillance systems and control strategies. We developed a spatial epidemiological model of ASFv transmission in wild pigs, which contributes to ASFv persistence in countries where wild pig populations are widespread. We evaluated the impacts of a realistic set of epidemiological traits including incubation period, infectious period, disease-induced mortality rate, and length of immunity on spatial transmission dynamics under different ecological conditions for the host population (i.e. host density). We analyze effects of these conditions on outbreak metrics using boosted regression models with response variables: peak incidence, rate of spatial spread, seroprevalence and area invaded after one year, and probability that an outbreak will occur. We found that the infectious period of living individuals is the most important predictor at all pig densities for peak incidence and the area affected at one year, followed closely by the incubation period of the virus. We discuss considerations for surveillance and control strategies for different genotypes of ASFv.

ecology↗

bioRxiv2025

Determinants of variation in epidemiological parameters for African Swine Fever virus

African Swine Fever (ASF) is a highly infectious reportable disease of swine that can have devastating consequences for pork producers and consumers. ASF virus can persist in either domestic or wild swine through several epidemiological cycles. This has led to a wide variety of epidemiological traits, making it challenging to plan effective surveillance and mitigation strategies. Here, we compile and analyze data from experimental infections of ASF virus variants from genotype II that have been reported in peer-reviewed publications. We provide descriptive summaries of the distributions of epidemiological parameters such as incubation period, infectious period, mortality rate, and R0 and develop predictive models that explain the variation in these quantities based on detection assays and other experimental design features. Our results provide a comprehensive perspective of estimates of epidemiological parameters for ASFV, allowing for increased transparency in accounting for parameter uncertainty in ASF preparedness modeling. Our meta-analysis also provides insight on knowledge gaps and study design issues that could be addressed by future experimentation.

immunology↗

bioRxiv2024

Comparing efficiencies of population control methods for responding to foreign animal disease threats in wild pigs

Introductions of foreign animal diseases (FADs) into free-ranging wildlife can be difficult to control and devastating for domestic livestock trade. Combating a new FAD introduction in wildlife with an emergency response requires quickly limiting spread of the disease by intensely removing wild animals and recovering their carcasses for proper disposal. In the case of African swine fever virus (ASFv) in wild pigs (Sus scrofa), which has been spreading in many regions of the world, there is little information on the time- and cost-efficiency of methods for intensively and consistently removing wild pigs and recovering carcasses in an emergency response scenario. We compared the efficiencies of aerial operations, trapping, an experimental toxic bait, and ground shooting in northcentral Texas, USA during two months in 2023. Removing and recovering carcasses of wild pigs averaged a rate of 0.15 wild pigs/person hour and cost an average of $233.04/wild pig ($USD 2023) across all four methods. Aerial operations required the greatest initial investment but subsequently was the most time- and cost-efficient, costing an average of $7,266 to incrementally reduce the population by 10% including recovering carcasses. Aerial operations required a ground crew of [~]7 people/helicopter to recover carcasses. Costs for reducing the population of wild pigs using trapping were similar, although took 13.5 times longer to accomplish. A benefit of trapping was carcass recovery was incorporated. Toxic baiting was less efficient because carcass recovery required substantial time, and we removed very few wild pigs with ground shooting in this landscape. We recommend combining aerial and trapping methodologies to remove wild pigs and their carcasses efficiently and effectively during a FAD response. Overall, our findings can inform the preparation of resources, personnel needs, and deployment readiness for FAD responses involving wild pigs.

ecology↗

bioRxiv2024

Torque Teno Sus Virus 1: A Potential Surrogate Pathogen to Study Pig-Transmitted Transboundary Animal Diseases

Understanding the epidemiology and transmission dynamics of transboundary animal diseases (TADs) among wild pigs (Sus scrofa) will aid in preventing the introduction or containment of TADs among wild populations. Given challenges associated with studying TADs in free-ranging populations, a surrogate pathogen system for in situ studies of pathogen dynamics would be ideal to elucidate how pathogens may circulate and be maintained within populations, how they may spillover into domestic populations, and how disease spread may be mitigated. We assessed the suitability of Torque teno sus virus 1 (TTSuV1) to serve as a surrogate pathogen for molecular epidemiological studies in wild pigs by investigating the prevalence, persistence, correlation with host health status and genetic variability at two study areas: Archbolds Buck Island Ranch in Florida and Savannah River Site in South Carolina. We then conducted a molecular epidemiological case study within the Archbolds Buck Island Ranch site to determine how analysis of this pathogen could inform transmission studies. Prevalence was high at both study areas (40%, n = 190). Phylogenetic analyses revealed high levels of genetic variability within and between study sites. Our case study showed that pairwise host relatedness and geographic distance were highly correlated to pairwise viral genetic similarity. Molecular epidemiological analyses revealed a distinct pattern of direct transmission from pig to pig occurring within and between family groups. Our results suggest TTSuV1 is highly suitable for molecular epidemiological analyses and will be useful for future in situ studies of transmission dynamics in wild pigs.

ecology↗

bioRxiv2023

What is Known, Unknown, and Needed to be Known about Damage Caused by Wild Pigs

Damage assessments provide evidence for initiating and evaluating management programs that protect natural resources and human livelihoods against invasive species. Wild pigs (Sus scrofa) cause extensive damage in their native and non-native ranges, but the extent of current damage and efficacy of management of the damage (i.e., population control of wild pigs, exclusion fencing, etc.) remains poorly described. We conducted a systematic review of physical damage caused by wild pigs to summarize what is known and identify knowledge gaps for damage assessment. Wild pig damage assessments have been overwhelmingly qualitative (84% of studies) and measured differently across studies, which prevents the determination of typical damage amounts to a particular resource and comparison across studies. Key priorities going forward are to standardize damage assessments quantitatively and measure population density (or index of such) of wild pigs concurrently with damage assessments to determine the relationship between damage and population levels. We provide a framework for inferring damage in new areas and assessing the benefits of management - to evaluate and optimize landscape-scale management programs. Overall, we recommend future studies strive for: 1) report the amount of damages in a standardized fashion (e.g., area damaged/area surveyed), 2) evaluate and report the amount of damage relative to the density of wild pigs, and 3) when reporting economic costs of damages incurred and management actions, describe the economic valuation method used along with the year of reference for the valuation. Capturing these elements are necessary steps to predict the benefits of management for an area with particular profile of resources and wild pig density, even in areas where damage assessments are not available. Meeting these criteria with allow for more generalizable results that can inform managers across the nearly global distribution of wild pigs

ecology↗

bioRxiv2021

An efficient method of evaluating multiple concurrent management actions on invasive populations

Evaluation of the efficacy of management actions to control invasive species is crucial for maintaining funding and to provide feedback for the continual improvement of management efficiency. However, it is often difficult to assess the efficacy of control methods due to limited resources for monitoring. Many managers view effort on monitoring as effort taken away from performing management actions. We developed a method to estimate invasive species abundance, evaluate management effectiveness, and evaluate population growth overtime from a combination of removal activities (e.g., aerial gunning, trapping, ground shooting) using only data collected during removal efforts (the method of removal, the date, location, number of animals removed, and the effort). This dynamic approach allows for estimating abundance at discrete time points and the estimation of population growth between removal periods. We applied this method to removal data from Mingo National Wildlife Refuge in Missouri from December 2015 to September 2019, where the management objective is elimination. Populations of feral swine on Mingo NWR have fluctuated over time but showed more marked declines in the last 3-6 months of the time series. More dramatic declines were observed in the center of the refuge likely aided by reducing potential immigration from the rest of the refuge. To counteract population growth (from both births and immigration) the percent of the population of feral swine removed monthly must be greater than the growth rate. On average, we found that removing 10% of the population monthly had only a 50% chance of causing a population decline, whereas removing 15% of the population monthly had a 95% chance of causing a population decline. Our method provides advancement over traditional removal modeling approaches because it can be applied to evaluate management programs that use a broad range of removal techniques concurrently and whose management effort and spatial coverage vary across time.

ecology↗

bioRxiv2019

Variation in host home range decreases rabies vaccination effectiveness by increasing the spatial spread of rabies

O_LIAnimal movement influences the spatial spread of wildlife infectious diseases through host-host contact structure and hence pathogen transmission. Wildlife disease hosts vary in characteristics related to pathogen transmission, which can increase the spread and intensity of disease outbreaks. The consequences of home range size variation on wildlife disease dynamics are poorly understood, but could help to predict disease spread and determine more effective disease management strategies.\nC_LIO_LIWe developed a spatially-explicit individual-based model to examine the effect of variation in host home range size on the spatial spread rate, persistence, and incidence of rabies virus (RABV) in raccoons (Procyon lotor). We tested the hypothesis that host home range area variation decreases vaccination effectiveness in wildlife host populations following pathogen invasion into a vaccination zone.\nC_LIO_LIWe simulated raccoon demography and RABV dynamics across a range of magnitudes and variances in weekly home range radius distributions for raccoons, and compared results to conditions that assumed a fixed host home range area. We examined how variable host home range radius distributions influenced the relative effectiveness of three components of orally-baited raccoon RABV vaccination (ORV) programs--timing and frequency of bait delivery, width of the zone where ORV baits were delivered, and proportion of hosts immunized.\nC_LIO_LIVariability in home range radius distributions increased RABV spread rates by 1.2 - 5.2-fold compared to simulations with fixed radii. More variable host home range radius distributions decreased relative vaccination effectiveness by 71% compared to less variable host home range radius distributions under conventional vaccination conditions. We found that vaccination timing was more influential for vaccination effectiveness than vaccination frequency or vaccination zone width.\nC_LIO_LIOur results suggest that variation in wildlife home range exploration increases the spatial spread and incidence of wildlife disease. Our vaccination results underscore the importance of prioritizing individual-level space use data collection to understand the dynamics of wildlife diseases and plan their effective control and elimination.\nC_LI

ecology↗

bioRxiv2019

Optimal spatial prioritization of control resources for elimination of invasive species under demographic uncertainty

Populations of invasive species often spread heterogeneously across a landscape, consisting of local populations that cluster in space but are connected by dispersal. A fundamental dilemma for invasive species control is how to optimally allocate limited fiscal resources across local populations. Theoretical work based on perfect knowledge of demographic connectivity suggests that targeting local populations from which migrants originate (sources) can be optimal. However, demographic processes such as abundance and dispersal can be highly uncertain, and the relationship between local population density and damage costs (damage function) is rarely known. We used a metapopulation model to understand how observational uncertainty in abundance and connectivity, and imperfect knowledge of the damage function, affect return on investment (ROI) for optimal control strategies. Budget, observational uncertainty, and the damage function had strong effects on the optimal resource allocation strategy. Uncertainty in dispersal probability was the least important determinant of ROI. The damage function determined which resource prioritization strategy was optimal when connectivity was symmetric but not when it was asymmetric. When connectivity was asymmetric, prioritizing source populations had a higher ROI than allocating effort equally across local populations, regardless of the damage function, but uncertainty in connectivity structure and abundance reduced ROI of the optimal prioritization strategy by 57% on average depending on the control budget. With low budgets (monthly removal rate of 6.7% of population), there was little advantage to prioritizing resources, especially when connectivity was high or symmetric, and observational uncertainty had only minor effects on ROI. Allotting funding for improved monitoring appeared to be most important when budgets were moderate (monthly removal of 13-20% of the population). Our result showed that multiple sources of observational uncertainty should be considered concurrently for optimizing ROI. Accurate estimates of connectivity direction and abundance were more important than accurate estimates of dispersal rates. Developing cost-effective surveillance methods to reduce observational uncertainties, and quantitative frameworks for determining how resources should be spatially apportioned to multiple monitoring and control activities are important and challenging future directions for optimizing ROI for invasive species control programs.

ecology↗

bioRxiv2019

Epidemic growth rates and host movement patterns shape management performance for pathogen spillover at the wildlife-livestock interface

AO_SCPCAPBSTRACTC_SCPCAPManaging pathogen spillover at the wildlife-livestock interface is a key step toward improving global animal health, food security, and wildlife conservation. However, predicting the effectiveness of management actions across host-pathogen systems with different life histories is an on-going challenge since data on intervention effectiveness are expensive to collect and results are system-specific. We developed a simulation model to explore how the efficacies of different management strategies vary according to host movement patterns and epidemic growth rates. The model suggested that fast-growing, fast-moving epidemics like avian influenza were best-managed with actions like biosecurity or containment, which limited and localized overall spillover risk. For fast-growing, slower-moving diseases like foot-and-mouth disease, depopulation or prophylactic vaccination were competitive management options. Many actions performed competitively when epidemics grew slowly and host movements were limited, and how management efficacy related to epidemic growth rate or host movement propensity depended on what objective was used to evaluate management performance. This framework may be a useful step in advancing how we classify and prioritise responses to novel pathogen spillover threats, and evaluate current management actions for pathogens emerging at the wildlife-livestock interface.

epidemiology↗