Reduced vertebrate diversity independent of spatial scale following feral swine invasions

Biological invasions often have contrasting consequences with reports of invasions decreasing diversity at small scales and facilitating diversity at large scales. Thus, previous literature has concluded that invasions have a fundamental spatial scale‐dependent relationship with diversity. Whether the scale‐dependent effects apply to vertebrate invaders is questionable because studies consistently report that vertebrate invasions produce different outcomes than plant or invertebrate invasions. Namely, vertebrate invasions generally have a larger effect size on species richness and vertebrate invaders commonly cause extinction, whereas extinctions are rare following invertebrate or plant invasions. In an agroecosystem invaded by a non‐native ungulate (i.e., feral swine, Sus scrofa), we monitored species richness of native vertebrates in forest fragments ranging across four orders of magnitude in area. We tested three predictions of the scale‐dependence hypothesis: (a) Vertebrate species richness would positively increase with area, (b) the species richness y‐intercept would be lower when invaded, and (c) the rate of native species accumulation with area would be steeper when invaded. Indeed, native vertebrate richness increased with area and the species richness was 26% lower than should be expected when the invasive ungulate was present. However, there was no evidence that the relationship was scale dependent. Our data indicate the scale‐dependent effect of biological invasions may not apply to vertebrate invasions.     

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.     

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.     

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.     

Interspecific interactions between feral pigs and native birds reveal both positive and negative effects

In tropical Australian rainforests, predators and scavengers aggregate beneath emergent trees that house large colonies of metallic starlings (Aplonis metallica), feeding in the nutrient‐rich open areas below. Analysis of camera‐trap records shows that the presence of feral pigs (Sus scrofa) is associated with an absence of birds (cockatoos and brush turkeys), presumably reflecting behavioural avoidance (pigs pose a direct danger to birds). However, bird numbers increase as soon as pigs depart, then fall if pigs are absent for long periods. Feral pigs thus displace native birds from these resource hotspots; but by turning over the soil and enhancing the birds' access to food, the pigs also have a positive impact on food availability for the avifauna. Thus, although invasive species have caused irreparable environmental damages worldwide, they may also provide positive benefits for certain species. The net benefit of such interspecific interactions will depend on the outcome of both positive and negative effects.     

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.     

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.     

Genetic patterns across multiple introductions of the globally invasive crab genus Carcinus

The European green crab Carcinus maenas is one of the world's most successful aquatic invaders, having established populations on every continent with temperate shores. Here we describe patterns of genetic diversity across both the native and introduced ranges of C. maenas and its sister species, C. aestuarii, including all known non‐native populations. The global data set includes sequences from the mitochondrial cytochrome c oxidase subunit I gene, as well as multilocus genotype data from nine polymorphic nuclear microsatellite loci. Combined phylogeographic and population genetic analyses clarify the global colonization history of C. maenas, providing evidence of multiple invasions to Atlantic North America and South Africa, secondary invasions to the northeastern Pacific, Tasmania, and Argentina, and a strong likelihood of C. maenas × C. aestuarii hybrids in South Africa and Japan. Successful C. maenas invasions vary broadly in the degree to which they retain genetic diversity, although populations with the least variation typically derive from secondary invasions or from introductions that occurred more than 100 years ago.     

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.     

Going feral: Time and propagule pressure determine range expansion of Asian house geckos into natural environments

Upon establishment in a new area, invasive species may undergo a prolonged period of relatively slow population growth and spread, known as a lag period. Lag periods are, apparently, common in invasions, but studies of the factors that facilitate subsequent expansions are lacking in natural systems. We used 10 semi‐independent invasions of the Asian house gecko (Hemidactylus frenatus) to investigate which factors facilitate expansion of this human‐associated species across the urban–woodland interface. We conducted 590 surveys over 12 months on 10 transects running from the urban edge to 2 km into adjacent natural woodland. We recorded H. frenatus out to 2 km from the urban edge on nine of 10 transects, and at high abundance at many woodland sites. Body size, body condition, sex ratio and proportion of gravid females did not vary with distance from the urban edge, suggesting viable, self‐sustaining populations in natural habitats. The extent of expansion was, however, strongly dependent on propagule pressure (the abundance of H. frenatus at the urban edge), and time (time since H. frenatus established in the urban area). The size of the urban area and the structure of the surrounding environment did not impact invasion. Our results show that an invasive species that is deemed ‘human‐associated’ over most of its range is invading natural habitats, and propagule pressure strongly controls the lag time in this system, a finding that echoes results for establishment probability at larger scales.     

Effects of Wild Pig Disturbance on Forest Vegetation and Soils

In North America, wild pigs (Sus scrofa; feral pigs, feral swine, wild boars) are a widespread exotic species capable of creating large-scale biotic and abiotic landscape perturbations. Quantification of wild pig environmental effects has been particularly problematic in northern climates, where they occur only recently as localized populations at low densities. Between 2016 and 2017, we assessed short-term (within ~2 yrs of disturbance) effects of a low-density wild pig population on forest features in the central Lower Peninsula of Michigan, USA. We identified 16 8-ha sites using global positioning system locations from 7 radio-collared wild pigs for sampling. Within each site, we conducted fine-scale assessments at 81 plots and quantified potential disturbance by wild pigs. We defined disturbance as exposure of overturned soil, often resulting from rooting behavior by wild pigs. We quantified ground cover of plants within paired 1-m² frames at each plot, determined effects to tree regeneration using point-centered quarter sampling, and collected soil cores from each plot. We observed less percent ground cover of native herbaceous plants and lower species diversity, particularly for plants with a coefficient of conservatism ≥5, in plots disturbed by wild pigs. We did not observe an increase in colonization of exotic plants following disturbance, though the observed prevalence of exotic plants was low. Wild pigs did not select for tree species when rooting, and we did not detect any differences in regeneration of light- and heavy-seeded tree species between disturbed or undisturbed plots. Magnesium and ammonium content in soils were lower in disturbed plots, suggesting soil disturbance accelerated leaching of macronutrients, potentially altering nitrogen transformation. Our study suggested that disturbances by wild pigs, even at low densities, alters short-term native herbaceous plant diversity and soil chemistry. Thus, small-scale exclusion of wild pigs from vulnerable and rare plant communities may be warranted. © 2020 The Wildlife Society.     

Selective constraints in cold‐region wild boars may defuse the effects of small effective population size on molecular evolution of mitogenomes

Spatial range expansion during population colonization is characterized by demographic events that may have significant effects on the efficiency of natural selection. Population genetics suggests that genetic drift brought by small effective population size (N_e) may undermine the efficiency of selection, leading to a faster accumulation of nonsynonymous mutations. However, it is still unknown whether this effect might be balanced or even reversed by strong selective constraints. Here, we used wild boars and local domestic pigs from tropical (Vietnam) and subarctic region (Siberia) as animal model to evaluate the effects of functional constraints and genetic drift on shaping molecular evolution. The likelihood‐ratio test revealed that Siberian clade evolved significantly different from Vietnamese clades. Different datasets consistently showed that Siberian wild boars had lower Ka/Ks ratios than Vietnamese samples. The potential role of positive selection for branches with higher Ka/Ks was evaluated using branch‐site model comparison. No signal of positive selection was found for the higher Ka/Ks in Vietnamese clades, suggesting the interclade difference was mainly due to the reduction in Ka/Ks for Siberian samples. This conclusion was further confirmed by the result from a larger sample size, among which wild boars from northern Asia (subarctic and nearby region) had lower Ka/Ks than those from southern Asia (temperate and tropical region). The lower Ka/Ks might be due to either stronger functional constraints, which prevent nonsynonymous mutations from accumulating in subarctic wild boars, or larger N_e in Siberian wild boars, which can boost the efficacy of purifying selection to remove functional mutations. The latter possibility was further ruled out by the Bayesian skyline plot analysis, which revealed that historical N_e of Siberian wild boars was smaller than that of Vietnamese wild boars. Altogether, these results suggest stronger functional constraints acting on mitogenomes of subarctic wild boars, which may provide new insights into their local adaptation of cold resistance.     

Ready on arrival: Standing variation at a chromosomal inversion contributes to rapid adaptation in an invasive marine crab

In this issue of Molecular Ecology, Tepolt et al. (2021) illustrate how the genetic architecture of adaptation and life history influence invasive success. A marvel of many invasive species is that they are incredibly successful despite evolutionary expectations that they will have low adaptive potential and suffer inbreeding depression due to initially small founding population sizes. Determining the combinations of ecoevolutionary factors that permit this apparent “genetic paradox of invasions” is an ongoing endeavour of invasive species research. Tepolt et al. (2021) study the European green crab in its invasive range on the North American west coast. Following a single introduction into California, this crab quickly spread across a wide latitude gradient, despite low diversity in the original founding population. Adaptation of this crab to clinal variation in temperature appeared largely driven by an inferred chromosomal inversion. This inversion exists as a balanced polymorphism in the European home range of green crabs and is associated with thermal tolerance. Tepolt et al. (2021) therefore demonstrate that adaptive evolution post introduction need not be impeded by bottlenecks if variation at key parts of the genome is available and can be maintained in introduced populations. Moreover, Tepolt et al. (2021) show how chromosomal inversions acting as large-effect loci might facilitate rapid responses to selection in introduced populations.     

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations

The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine‐scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.     

Seed dispersal effectiveness by a large‐bodied invasive species in defaunated landscapes

Animal‐dispersed plants are increasingly reliant on effective seed dispersal provided by small‐bodied frugivores in defaunated habitats. In the Neotropical region, the non‐native wild pig (Sus scrofa) is expanding its distribution and we hypothesized that they can be a surrogate for seed dispersal services lost by defaunation. We performed a thorough analysis of their interaction patterns, interaction frequencies, seed viability, and characteristics of the seed shadows they produce. We found 15,087 intact seeds in 56% of the stomachs and 5,186 intact seeds in 90% of the scats analyzed, 95% of which were smaller than 10 mm in diameter. Wild pigs were the third most effective disperser among 21 extant frugivore species in a feeding trail experiment in terms of quantity of seeds removed. Gut retention time was 70 ± 23 hr, indicating wild pigs can promote long‐distance seed dispersal. Seed survival after seed handling and gut passage by wild pigs was positively related with seed size, but large seeds were spat out and only smaller seeds were defecated intact, for which we observed a positive or neutral effect on germination relative to manually de‐pulped seeds. Finally, deposition of seeds was four times more frequent in unsuitable than suitable sites for seedling recruitment and establishment. Seed dispersal effectiveness by wild pigs is high in terms of the quantity of seeds dispersed but variable in terms of the quality of the service provided. Our study highlights that negative and positive effects delivered by non‐native species should be examined in a case by case scenario. Abstract in Portuguese is available with online material.