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.     

Modeling ecological traps for the control of feral pigs

Ecological traps are habitat sinks that are preferred by dispersing animals but have higher mortality or reduced fecundity compared to source habitats. Theory suggests that if mortality rates are sufficiently high, then ecological traps can result in extinction. An ecological trap may be created when pest animals are controlled in one area, but not in another area of equal habitat quality, and when there is density‐dependent immigration from the high‐density uncontrolled area to the low‐density controlled area. We used a logistic population model to explore how varying the proportion of habitat controlled, control mortality rate, and strength of density‐dependent immigration for feral pigs could affect the long‐term population abundance and time to extinction. Increasing control mortality, the proportion of habitat controlled and the strength of density‐dependent immigration decreased abundance both within and outside the area controlled. At higher levels of these parameters, extinction was achieved for feral pigs. We extended the analysis with a more complex stochastic, interactive model of feral pig dynamics in the Australian rangelands to examine how the same variables as the logistic model affected long‐term abundance in the controlled and uncontrolled area and time to extinction. Compared to the logistic model of feral pig dynamics, the stochastic interactive model predicted lower abundances and extinction at lower control mortalities and proportions of habitat controlled. To improve the realism of the stochastic interactive model, we substituted fixed mortality rates with a density‐dependent control mortality function, empirically derived from helicopter shooting exercises in Australia. Compared to the stochastic interactive model with fixed mortality rates, the model with the density‐dependent control mortality function did not predict as substantial decline in abundance in controlled or uncontrolled areas or extinction for any combination of variables. These models demonstrate that pest eradication is theoretically possible without the pest being controlled throughout its range because of density‐dependent immigration into the area controlled. The stronger the density‐dependent immigration, the better the overall control in controlled and uncontrolled habitat combined. However, the stronger the density‐dependent immigration, the poorer the control in the area controlled. For feral pigs, incorporating environmental stochasticity improves the prospects for eradication, but adding a realistic density‐dependent control function eliminates these prospects.     

Detection and persistence of environmental DNA from an invasive,terrestrial mammal

Invasive Sus scrofa, a species commonly referred to as wild pig or feral swine, is a destructive invasive species with a rapidly expanding distribution across the United States. We used artificial wallows and small waterers to determine the minimum amount of time needed for pig eDNA to accumulate in the water source to a detectable level. We removed water from the artificial wallows and tested eDNA detection over the course of 2 weeks to understand eDNA persistence. We show that our method is sensitive enough to detect very low quantities of eDNA shed by a terrestrial mammal that has limited interaction with water. Our experiments suggest that the number of individuals shedding into a water system can affect persistence of eDNA. Use of an eDNA detection technique can benefit management efforts by providing a sensitive method for finding even small numbers of individuals that may be elusive using other methods.     

Less can be more: loss of MHC functional diversity can reflect adaptation to novel conditions during fish invasions

The ability of invasive species to adapt to novel conditions depends on population size and environmental mismatch, but also on genetic variation. Away from their native range, invasive species confronted with novel selective pressures may display different levels of neutral versus functional genetic variation. However, the majority of invasion studies have only examined genetic variation at neutral markers, which may reveal little about how invaders adapt to novel environments. Salmonids are good model systems to examine adaptation to novel pressures because they have been translocated all over the world and represent major threats to freshwater biodiversity in the Southern Hemisphere, where they have become invasive. We examined patterns of genetic differentiation at seven putatively neutral (microsatellites) loci and one immune‐related major histocompatibility complex (MHC class II‐β) locus among introduced rainbow trout living in captivity (farmed) or under natural conditions (naturalized) in Chilean Patagonia. A significant positive association was found between differentiation at neutral and functional markers, highlighting the role of neutral evolutionary forces in shaping genetic variation at immune‐related genes in salmonids. However, functional (MHC) genetic diversity (but not microsatellite diversity) decreased with time spent in the wild since introduction, suggesting that there was selection against alleles associated with captive rearing of donor populations that do not provide an advantage in the wild. Thus, although high genetic diversity may initially enhance fitness in translocated populations, it does not necessarily reflect invasion success, as adaptation to novel conditions may result in rapid loss of functional MHC diversity.     

Evaluation of fences for containing feral swine under simulated depopulation conditions

Populations of feral swine (Sus scrofa) are estimated to include >2 million animals in the state of Texas, USA, alone. Feral swine damage to property, crops, and livestock exceeds $50 million annually. These figures do not include the increased risks and costs associated with the potential for feral swine to spread disease to domestic livestock. Thus, effective bio-security measures will be needed to quickly isolate affected feral swine populations during disease outbreaks. We evaluated enclosures built of 0.86-m-tall traditional hog panels for containing feral swine during 35 trials, each involving 6 recently caught animals exposed to increasing levels of motivation. During trials, fences were 97% successful when enclosures were entered by humans for maintenance purposes; 83% effective when pursued by walking humans discharging paintball projectors; and in limited testing, 100% successful when pursued and removed by gunners in a helicopter. In addition to being effective in containing feral swine, enclosures constructed of hog panels required simple hand tools, took <5 min/m to erect, and were inexpensive ($5.73/m excluding labor) relative to other fencing options. As such, hog-panel fences are suitable for use by state and federal agencies for rapid deployment in disease response situations, but also exhibit utility for general control of other types of damage associated with feral swine. © 2011 The Wildlife Society.     

Vegetation Recovery 16 Years after Feral Pig Removal from a Wet Hawaiian Forest

Nonnative ungulates can alter the structure and function of forest ecosystems. Feral pigs in particular pose a substantial threat to native plant communities throughout their global range. Hawaiian forests are exceptionally vulnerable to feral pig activity because native vegetation evolved in the absence of large mammalian herbivores. A common approach for conserving and restoring forests in Hawaii is fencing and removal of feral pigs. The extent of native plant community recovery and nonnative plant invasion following pig removal, however, is largely unknown. Our objective was to quantify changes in native and nonnative understory vegetation over a 16 yr period in adjacent fenced (pig‐free) vs. unfenced (pig‐present) Hawaiian montane wet forest. Native and nonnative understory vegetation responded strongly to feral pig removal. Density of native woody plants rooted in mineral soil increased sixfold in pig‐free sites over 16 yr, whereas establishment was almost exclusively restricted to epiphytes in pig‐present sites. Stem density of young tree ferns increased significantly (51.2%) in pig‐free, but not pig‐present sites. Herbaceous cover decreased over time in pig‐present sites (67.9%). In both treatments, number of species remained constant and native woody plant establishment was limited to commonly occurring species. The nonnative invasive shrub, Psidium cattleianum, responded positively to release from pig disturbance with a fivefold increase in density in pig‐free sites. These results suggest that while common native understory plants recover within 16 yr of pig removal, control of nonnative plants and outplanting of rarer native species are necessary components of sustainable conservation and restoration efforts in these forests.     

Rapid evolution of body fluid regulation following independent invasions into freshwater habitats

Colonizations from marine to freshwater environments constitute among the most dramatic evolutionary transitions in the history of life. Colonizing dilute environments poses great challenges for acquiring essential ions against steep concentration gradients. This study explored the evolution of body fluid regulation following freshwater invasions by the copepod Eurytemora affinis. The goals of this study were to determine (1) whether invasions from saline to freshwater habitats were accompanied by evolutionary shifts in body fluid regulation (hemolymph osmolality) and (2) whether parallel shifts occurred during independent invasions. We measured hemolymph osmolality for ancestral saline and freshwater invading populations reared across a range of common-garden salinities (0.2-25 PSU). Our results revealed the evolution of increased hemolymph osmolality (by 16-31%) at lower salinities in freshwater populations of E. affinis relative to their saline ancestors. Moreover, we observed the same evolutionary shifts across two independent freshwater invasions. Such increases in hemolymph osmolality are consistent with evidence of increased ion uptake in freshwater populations at low salinity, found in a previous study, and are likely to entail increased energetic costs upon invading freshwater habitats. Our findings are consistent with the evolution of increased physiological regulation accompanying transitions into stressful environments.     

Population genomic,olfactory, dietary,and gut microbiota analyses demonstrate the unique evolutionary trajectory of feral pigs

Domestication is an intriguing evolutionary process. Many domestic populations are subjected to strong human-mediated selection, and when some individuals return to the wild, they are again subjected to selective forces associated with new environments. Generally, these feral populations evolve into something different from their wild predecessors and their members typically possess a combination of both wild and human selected traits. Feralisation can manifest in different forms on a spectrum from a wild to a domestic phenotype. This depends on how the rewilded domesticated populations can readapt to natural environments based on how much potential and flexibility the ancestral genome retains after its domestication signature. Whether feralisation leads to the evolution of new traits that do not exist in the wild or to convergence with wild forms, however, remains unclear. To address this question, we performed population genomic, olfactory, dietary, and gut microbiota analyses on different populations of Sus scrofa (wild boar, hybrid, feral and several domestic pig breeds). Porcine single nucleotide polymorphisms (SNPs) analysis shows that the feral population represents a cluster distinctly separate from all others. Its members display signatures of past artificial selection, as demonstrated by values of F_ST in specific regions of the genome and bottleneck signature, such as the number and length of runs of homozygosity. Generalised F_ST values, reacquired olfactory abilities, diet, and gut microbiota variation show current responses to natural selection. Our results suggest that feral pigs are an independent evolutionary unit which can persist so long as levels of human intervention remain unchanged.     

Maternal genomic variability of the wild boar (Sus scrofa) reveals the uniqueness of East‐Caucasian and Central Italian populations

The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East‐Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the presence of old maternal lineages in two Southern glacial refugia (i.e., Caucasus and the Italian peninsula), as a legacy of an ancient wave of colonization of Southern Europe from an Eastern origin.     

Invasive species removal increases species and phylogenetic diversity of wetland plant communities

Plant invasions result in biodiversity losses and altered ecological functions, though quantifying loss of multiple ecosystem functions presents a research challenge. Plant phylogenetic diversity correlates with a range of ecosystem functions and can be used as a proxy for ecosystem multifunctionality. Laurentian Great Lakes coastal wetlands are ideal systems for testing invasive species management effects because they support diverse biological communities, provide numerous ecosystem services, and are increasingly dominated by invasive macrophytes. Invasive cattails are among the most widespread and abundant of these taxa. We conducted a three‐year study in two Great Lakes wetlands, testing the effects of a gradient of cattail removal intensities (mowing, harvest, complete biomass removal) within two vegetation zones (emergent marsh and wet meadow) on plant taxonomic and phylogenetic diversity. To evaluate native plant recovery potential, we paired this with a seed bank emergence study that quantified diversity metrics in each zone under experimentally manipulated hydroperiods. Pretreatment, we found that wetland zones had distinct plant community composition. Wet meadow seed banks had greater taxonomic and phylogenetic diversity than emergent marsh seed banks, and high‐water treatments tended to inhibit diversity by reducing germination. Aboveground harvesting of cattails and their litter increased phylogenetic diversity and species richness in both zones, more than doubling richness compared to unmanipulated controls. In the wet meadow, harvesting shifted the community toward an early successional state, favoring seed bank germination from early seral species, whereas emergent marsh complete removal treatments shifted the community toward an aquatic condition, favoring floating‐leaved plants. Removing cattails and their litter increased taxonomic and phylogenetic diversity across water levels, a key environmental gradient, thereby potentially increasing the multifunctionality of these ecosystems. Killing invasive wetland macrophytes but leaving their biomass in situ does not address their underlying mechanism of dominance and is less effective than more intensive treatments that also remove their litter.     

Spread of an introduced parasite across the Hawaiian archipelago independent of its introduced host

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Signatures of de‐domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution

Autochthonous pig breeds are usually reared in extensive or semi‐extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo‐Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south‐eastern European countries (Kr?kopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro‐geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild‐type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of ‘de‐domestication’ process, and wild resources are challenged by a ‘domestication’ drift. Both need to be further investigated and managed.     

Feral horse impacts on threatened plants and animals in sub‐alpine and montane environments in Victoria,Australia

Feral herbivores are a major driver of biodiversity loss globally and can alter the structure, composition and functioning of ecosystems. The direct impacts of feral herbivores on plant communities are well studied, but the direct and indirect effect they have on wildlife is not well understood. In Victoria (south‐eastern Australia), a large feral Horse (Equus caballus) population coincides with highly sensitive and nationally endangered Alpine Sphagnum Bogs and Associated Fens communities, and several threatened animal species. We assessed the impact of feral horses on this ecological community and the Alpine Water Skink (Eulamprus kosciuskoi) and the Broad‐toothed Rat (Mastacomys fuscus) at 20 sites with varying levels of horse disturbance. We used scat counts to determine an index of feral horse abundance and quantified impacts associated with their presence in the landscape. Active searches were used for Alpine Water Skink and scat and runway surveys for Broad‐toothed Rat. We also measured the vegetation structure and the abundance of different vegetation types (life forms). Our results suggest that feral horses are associated with vegetation types and characteristics that negatively influence the presence or abundance of Alpine Water Skink and Broad‐toothed Rat. Sites with high horse activity had more low‐growing forbs, and the abundance of Alpine Water Skink was negatively related to this vegetation type. Grasses, sedges, rushes and shrubs were also less dense and lower in height in high horse activity sites, and Broad‐toothed Rat was less likely to be present in areas with these habitat attributes. We recommend that feral horses are controlled to protect these threatened vertebrate species and their Sphagnum bog habitat.     

Continental‐scale analysis of feral cat diet in Australia,prey‐switching and the risk: benefit of rabbit control

Recent analyses of geographical variation in cats’ diet across Australia have been used to highlight rabbit control as a conservation risk, on the basis that prey‐switching by cats following rabbit control is likely to threaten Australian fauna. There is no direct evidence to support that proposition. However, there is direct evidence of repeated prey‐switching due to seasonal fluctuations in uncontrolled rabbit populations, of long‐term suppression of rabbit numbers by effective rabbit control, and that reduced rabbit abundance leads to reduced cat abundance, reduced predation of native fauna and recovery of threatened prey populations. Furthermore, rabbits are a known threat to many Australian native plants and rabbit control has proven benefits for their recovery, thereby offering long‐term benefits for dependent fauna and broader ecosystem function. On the balance of evidence, rabbit control should be encouraged in Australia wherever possible, as a national conservation priority.