Characterizing feral swine movement across the contiguous United States using neural networks and genetic data

Globalization has led to the frequent movement of species out of their native habitat. Some of these species become highly invasive and capable of profoundly altering invaded ecosystems. Feral swine (Sus scrofa × domesticus) are recognized as being among the most destructive invasive species, with populations established on all continents except Antarctica. Within the United States (US), feral swine are responsible for extensive crop damage, the destruction of native ecosystems, and the spread of disease. Purposeful human-mediated movement of feral swine has contributed to their rapid range expansion over the past 30 years. Patterns of deliberate introduction of feral swine have not been well described as populations may be established or augmented through small, undocumented releases. By leveraging an extensive genomic database of 18,789 samples genotyped at 35,141 single nucleotide polymorphisms (SNPs), we used deep neural networks to identify translocated feral swine across the contiguous US. We classified 20% (3364/16,774) of sampled animals as having been translocated and described general patterns of translocation using measures of centrality in a network analysis. These findings unveil extensive movement of feral swine well beyond their dispersal capabilities, including individuals with predicted origins >1000 km away from their sampling locations. Our study provides insight into the patterns of human-mediated movement of feral swine across the US and from Canada to the northern areas of the US. Further, our study validates the use of neural networks for studying the spread of invasive species.

Swine global genomic resources: insights into wild and domesticated populations

Suids, both domesticated and wild, are found on all continents except for Antarctica and provide valuable food resources for humans in addition to serving as important models for biomedical research. Continuing advances in genome sequencing have allowed researchers to compare the genomes from diverse populations of suids helping to clarify their evolution and dispersal. Further analysis of these samples may provide clues to improve disease resistance/resilience and productivity in domestic suids as well as better ways of classifying and conserving genetic diversity within wild and captive suids. Collecting samples from diverse populations of suids is resource intensive and may negatively impact endangered populations. Here we catalog extensive tissue and DNA samples from suids in collections in both Europe and North America. We include samples that have previously been used for whole genome sequencing, targeted DNA sequencing, RNA sequencing, and reduced representation bisulfite sequencing (RRBS). This work provides an important centralized resource for researchers who wish to access published databases.

Assessing population structure and migration patterns of wild boar (Sus scrofa) in Japan

Geographical wildlife patterns reflect historical range expansion and connectivity and provide insights into wildlife population management. In our large-scale phylogeographic population analysis of wild boars (Sus scrofa leucomystax) in Japan, we identified 15 clusters using 29 microsatellite markers, each structured within a range of approximately 200 km. This suggests that evolution was essentially driven by isolation by distance, and that the range of gene flow was limited. One cluster contained subpopulations located approximately 900 km apart, indicating the occurrence of past anthropogenic introductions. Moreover, we estimated effective migration to visualize the geographic genetic population diversity. This analysis identified six potential barriers, one of which involved large plains and mountainous areas in the Kanto region of eastern Japan. This barrier likely persisted in the two eastern clusters for an extended period, restricting migration to the neighboring areas. Overall, our study sheds light on the demographic history of wild boar in Japan, provides evidence of past anthropogenic introductions from distant areas, and highlights the importance of geographic barriers in shaping genetic diversity and population dynamics. This knowledge will be beneficial for forming informed wildlife management strategies toward the conservation of genetic integrity and ecological balance of wild boar populations in Japan.

Multiscale landscape genetic analysis identifies major waterways as a barrier to dispersal of feral pigs in north Queensland, Australia

Feral pigs (Sus scrofa) are a destructive and widespread invasive pest in Australia. An understanding of feral pig movement is required to develop management strategies to control feral pigs in Australia. Because landscape structure can have a strong influence on animal movement, it is important to determine how landscape features facilitate or impede the movement of feral pigs. Consequently, we conducted a landscape genetic analysis of feral pig populations in the Herbert region of far north Queensland, Australia, to determine management units and provide recommendations to better inform feral pig population control strategies. Using microsatellite data obtained from 256 feral pig samples from 44 sites, we examined feral pig population structure at multiple spatial scales for univariate and multivariate landscape resistance surfaces to determine the optimal spatial scale and to identify which of the nine landscape features tested impede or facilitate feral pig gene flow. Only weak genetic structure was found among the 44 sampling sites, but major waterways were identified as a minor barrier to gene flow, and an isolation by distance model was supported. We also found that highways facilitated gene flow across the study area, and this suggests that they may act as movement corridors or indicate translocation of feral pigs. Additionally, incorporating a second spatial scale enhanced the ability of our landscape genetics analysis to detect the influence of landscape structure on gene flow. We identified three management units based on natural barriers to gene flow and future targeted control should be undertaken in these management units to deliver sustained reduction of feral pig populations in the Herbert region. This study demonstrates how a landscape genetic approach can be used to gain insight into the ecology of an invasive pest species and be used to develop population control strategies which utilise natural barriers to movement.

From chip to SNP: Rapid development and evaluation of a targeted capture genotyping-by-sequencing approach to support research and management of a plaguing rodent

The management of invasive species has been greatly enhanced by population genetic analyses of multilocus single-nucleotide polymorphism (SNP) datasets that provide critical information regarding pest population structure, invasion pathways, and reproductive biology. For many applications there is a need for protocols that offer rapid, robust and efficient genotyping on the order of hundreds to thousands of SNPs, that can be tailored to specific study populations and that are scalable for long-term monitoring schemes. Despite its status as a model laboratory species, there are few existing resources for studying wild populations of house mice (Mus musculus spp.) that strike this balance between data density and laboratory efficiency. Here we evaluate the utility of a custom targeted capture genotyping-by-sequencing approach to support research on plaguing house mouse populations in Australia. This approach utilizes 3,651 hybridization capture probes targeting genome-wide SNPs identified from a sample of mice collected in grain-producing regions of southeastern Australia genotyped using a commercially available microarray platform. To assess performance of the custom panel, we genotyped wild caught mice (N = 320) from two adjoining farms and demonstrate the ability to correctly assign individuals to source populations with high confidence (mean >95%), as well as robust kinship inference within sites. We discuss these results in the context of proposed applications for future genetic monitoring of house mice in Australia.

Cultural and regulatory factors influence distribution and trajectory of invasive species in the United States: A wild pig case study

Since 2012, control of invasive wild pigs (Sus scrofa) in the United States (US) has become a state and national priority due to their propensity to damage agricultural commodities and infrastructure, transmit disease, detrimentally affect ecological processes, and compete with native wildlife for resources. While several life-history characteristics certainly aided their proliferation, the recreational value of wild pigs was likely the stimulus for translocation and subsequent establishment of populations in ≥35 states, causing an annual economic burden of $1.5 billion in the US. Consequently, state-level legislative procedures regarding wild pigs are expanding in scope and priority, but policy among states lacks uniformity. States vary in their treatment of wild pig control based on differing resource appropriations and stakeholder interests. We conducted an evaluation to determine if policy was associated with state-level 1) presence of wild pigs, 2) spatial extent of wild pig population occupancy, and 3) trajectory of wild pig population occupancy. Our results suggest the presence of wild pigs in various states was influenced by hunting preserves and the sale of hunting opportunities. In occupied states, the spatial extent of wild pigs was again associated with the sale of hunting opportunities and a wild pig hunting culture. Finally, the trajectory of state-level wild pig spatial occupancy was positively influenced by the sale of hunting opportunities, and negatively influenced by transportation policies. Based on these findings, we propose state governments standardize transportation policy and fenced hunting regulations across regions of the US in a more prohibitive fashion to diminish range expansion through illegal and negligent introductions via transportation, release, and escapes from game farms. Moreover, in states where wild pigs have yet to establish, we strongly recommend states proactively prohibit transportation through intra- and interstate movement.

Evaluating potential sources of invasive wild pigs in Ontario

Invasive wild pigs (Sus scrofa) are considered one of the most damaging species globally, and once they become established in an area, they are notoriously difficult to eliminate. As such, identifying the potential pathways of invasion, especially in places with emerging populations, is critical for preventing new or continued invasion. Wild pigs have been reported in Ontario, Canada, in recent years. We tested four nonexclusive hypotheses about the source of wild pigs in Ontario: (a) escapees from captive sources within Ontario; (b) invasion from neighboring jurisdictions; (c) existing wild populations within Ontario; and (d) translocation and illegal release. We found that sightings of Eurasian wild boar were closer to premises with wild boar than were random locations; wild boar sightings were an average of 16.3 km (SD = 25.4 km, min = 0.2 km, n = 20) from premises with wild boar. We also found that sightings of domestic pigs were closer to domestic pig farms than expected. Sightings of wild pigs in groups of more than four animals were rare. Our results suggest that wild pigs observed in Ontario are recent escapes from captivity, recognizing that there may be established groups of wild pigs that we have not yet detected. While not common, we also received reports indicating that in the past, wild pigs have been translocated and illegally released. Other North American jurisdictions that have been successful at eliminating wild pigs have removed existing populations and changed regulations to limit future invasion, such as prohibiting possession and transport of wild boar and prohibiting hunting of wild pigs.

Population Genetics of the Invasive Red Fox, Vulpes vulpes, in South-Eastern Australia

The use of genetic information in conservation biology has become more widespread with genetic information more readily available for non-model organisms. It has also been recognized that genetic information from invasive species can inform their management and control. The red fox poses a significant threat to Australian native fauna and the agricultural industry. Despite this, there are few recently published studies investigating the population genetics of foxes in Australia. This study investigated the population genetics of 94 foxes across the Illawarra and Shoalhaven regions of New South Wales, Australia. Diversity Array sequencing technology was used to genotype a large number of single nucleotide polymorphisms (N = 33,375). Moderate genetic diversity and relatedness were observed across the foxes sampled. Low to moderate levels of inbreeding, high-levels of identity-by-state values, as well as high identity-by-descent values were also found. There was limited evidence for population genetic structure among the foxes across the landscape sampled, supporting the presence of a single population across the study area. This indicates that there may be no barriers hindering fox dispersal across the landscape.

Genetic Population Structure of Wild Pigs in Southern Texas

Simple Summary

Wild pigs are the most abundant wild exotic ungulate in the United States. In Texas, particularly, they are abundant and represent a threat to ecosystems, agriculture and humans. Our objective was to apply a landscape-scale analysis of population genetic structure of wild pigs to aid in their management in southern Texas. We used microsatellites to assist large-scale applied management. We found that some populations were isolated from one another. However, many individuals and local populations were admixed, which indicates that multiple introductions and artificial movement of individuals has occurred. Wild pig management efficiency and effectiveness may be able to improve if illegal translocations stop (e.g., enforcing laws) and if management cooperatives are created to manage spatially extensive areas of southern Texas.

Abstract

Wild pigs (Sus scrofa) alter ecosystems, affect the economy, and carry diseases that can be transmitted to livestock, humans, and wildlife. Understanding wild pig movements and population structure data, including natural population boundaries and dispersal, may potentially increase the efficiency and effectiveness of management actions. We trapped, conducted aerial shootings, and hunted wild pigs from 2005 to 2009 in southern Texas. We used microsatellites to assist large-scale applied management. We quantify broad-scale population structure among 24 sites across southern Texas by computing an overall F_ST value, and a Bayesian clustering algorithm both with and without considering the spatial location of samples. At a broad geographic scale, pig populations displayed a moderate degree of genetic structure (F_ST = 0.11). The best partition for number of populations, based on 2nd order rate of change of the likelihood distribution, was K = 10 genetic clusters. The spatially explicit Bayesian clustering algorithm produced similar results, with minor differences in designation of admixed sites. We found evidence of past (and possibly ongoing) translocations; many populations were admixed. Our original goal was to identify landscape features, such as barriers or dispersal corridors, that could be used to aid management. Unfortunately, the extensive admixture among clusters made this impossible. This research shows that large-scale management of wild pigs may be necessary to achieve control and ameliorate damages. Reduction or cessation of translocations is necessary to prevent human-mediated dispersion of wild pigs.

Factors and costs associated with removal of a newly established population of invasive wild pigs in Northern U.S

The human-mediated spread of exotic and invasive species often leads to unintentional and harmful consequences. Invasive wild pigs (Sus scrofa) are one such species that have been repeatedly translocated throughout the United States and cause extensive damage to natural ecosystems, threatened and endangered species, agricultural resources, and private lands. In 2005, a newly established population of wild pigs was confirmed in Fulton County, Illinois, U.S. In 2011, a state-wide wild pig damage management program involving federal, state, and local government authorities directed a concerted effort to remove wild pigs from the county until the last wild pig (of 376 total) was successfully removed in 2016. We examined surveillance data from camera traps at bait sites and records of wild pig removals during this elimination program to identify environmental and anthropogenic factors that optimized removal of this population. Our results revealed that wild pigs used bait sites most during evening and nocturnal periods and on days with lower daily maximum temperatures. Increased removals of wild pigs coincided with periods of cold weather. We also identified that fidelity and time spent at bait sites by wild pigs was not influenced by increasing removals of wild pigs. Finally, the costs to remove wild pigs averaged $50 per wild pig (6.8 effort hours per wild pig) for removing the first 99% of the animals. Cost for removing the last 1% increased 84-fold, and averaged 122.8 effort hours per wild pig removed. Our results demonstrated that increased effort in removing wild pigs using bait sites should be focused during periods of environmental stress to maximize removal efficiency. These results inform elimination programs attempting to remove newly established populations of wild pigs, and ultimately prevent population and geographic expansion.

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine

Invasive alien species are a significant threat to both economic and ecological systems. Identifying the processes that give rise to invasive populations is essential for implementing effective control strategies. We conducted an ancestry analysis of invasive feral swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is widely distributed throughout the contiguous United States, to describe introduction pathways, sources of newly emergent populations and processes contributing to an ongoing invasion. Comparisons of high-density single nucleotide polymorphism genotypes for 6,566 invasive feral swine to a comprehensive reference set of S. scrofa revealed that the vast majority of feral swine were of mixed ancestry, with dominant genetic associations to Western heritage breeds of domestic pig and European populations of wild boar. Further, the rapid expansion of invasive feral swine over the past 30 years was attributable to secondary introductions from established populations of admixed ancestry as opposed to direct introductions of domestic breeds or wild boar. Spatially widespread genetic associations of invasive feral swine to European wild boar deviated strongly from historical S. scrofa introduction pressure, which was largely restricted to domestic pigs with infrequent, localized wild boar releases. The deviation between historical introduction pressure and contemporary genetic ancestry suggests wild boar-hybridization may contribute to differential fitness in the environment and heightened invasive potential for individuals of admixed domestic pig-wild boar ancestry.

Use of environmental DNA (eDNA) in streams to detect feral swine (Sus scrofa)

Invasive feral swine can damage ecosystems, disrupt plant and animal populations, and transmit diseases. Monitoring of feral swine populations requires expensive and labor-intensive techniques such as aerial surveys, field surveys for sign, trail cameras, and verifying landowner reports. Environmental DNA (eDNA) provides an alternative method for locating feral swine. To aid in detection of this harmful invasive species, a novel assay was developed incorporating molecular methods. From August 2017 to April 2018, water samples and stream data were collected along 400 m transects in two different stream types where swine DNA was artificially introduced to investigate potential factors affecting detection. A generalized linear model (family binomial) was used to characterize environmental conditions affecting swine DNA detection; detection was the dependent variable and stream measurements included stream type, distance downstream, water temperature, velocity, turbidity, discharge, and pH as independent variables. Parameters from the generalized linear model were deemed significant if 95% confidence intervals did not overlap 0. Detection probability for swine DNA negatively related to water temperature (β =  − 0.21, 95% CI [−0.35 to −0.09]), with the highest detection probability (0.80) at 0 °C and lowest detection probability (0.05) at 17.9 °C water temperature. Results indicate that sampling for swine eDNA in free-flowing stream systems should occur at lower water temperatures to maximize detection probability. This study provides a foundation for further development of field and sampling techniques for utilizing eDNA as a viable alternative to monitoring a terrestrial invasive species in northern regions of the United States.

Getting Back to Nature: Feralization in Animals and Plants

Formerly domesticated organisms and artificially selected genes often escape controlled cultivation, but their subsequent evolution is not well studied. In this review, we examine plant and animal feralization through an evolutionary lens, including how natural selection, artificial selection, and gene flow shape feral genomes, traits, and fitness. Available evidence shows that feralization is not a mere reversal of domestication. Instead, it is shaped by the varied and complex histories of feral populations, and by novel selection pressures. To stimulate further insight we outline several future directions. These include testing how 'domestication genes' act in wild settings, studying the brains and behaviors of feral animals, and comparative analyses of feral populations and taxa. This work offers feasible and exciting research opportunities with both theoretical and practical applications.

Assessing public support for restrictions on transport of invasive wild pigs (Sus scrofa) in the United States

Wild pigs (Sus scrofa) are a non-native invasive species in the United States that cause significant economic loss, transmit disease, and inflict damage upon natural resources, agriculture, livestock, and property. Geographic distribution of wild pigs in the United States has nearly tripled since 1982, with anthropogenic influences playing a significant role in the expansion. In this regard, there is speculation that a driver of the expansion may be human-mediated movement of wild pigs to new areas for the purpose of sport hunting. In response, states have implemented a variety of wild pig control policies, including legal restrictions on their transport. The success of such policies depends, in part, on their level of public support, which in turn may be influenced by individuals' attitudes concerning wild pigs, their interest in maintaining wild pig populations (e.g., for sport hunting), and their knowledge and awareness of the threats wild pigs pose. Multiple regression was used to analyze data collected from a nationwide survey concerning attitudes toward wild pigs and policies that restrict their transport. Results indicate that a majority of individuals in the United States have negative attitudes toward wild pigs and support policies that restrict their transport and penalize transgressors. Consistent with other invasive species research, findings suggest that as knowledge and awareness of wild pigs increase, so too does support for policies restricting and penalizing transport of wild pigs. Contrary to previous studies, this research also finds that hunters are more likely to support restrictions on wild pig transport than are non-hunters. Overall, these findings suggest that legal restrictions on the transport of wild pigs, even in states with large hunter populations, enjoy broad public support and may help to curb the expansion of wild pig populations.