Divergence time estimates of East Asian and European pigs based on multiple near complete mitochondrial DNA sequences

The time since the divergence of European and East Asian domestic pigs and wild boars has been estimated in several phylogenetic analyses, generally based on partial mitochondrial sequences or on a small number of complete mtDNA sequences. In the present study, we obtained a refined estimate of this divergence time based on a set of 32 near‐complete mtDNA sequences from wild and domestic pigs of European and Asian types, including 14 new and 18 previously published sequences. A weighted average for different functional mtDNA components resulted in an estimate of 746 000 YBP for the divergence of Asian‐type from European‐type pigs. In addition, our data allowed us to estimate a divergence time between wild and domestic European pigs of 8500 YBP. However, it must be considered cautiously, as most of the estimated values of this sequence divergence were not different from zero, and isolation between wild and domestic pigs has never been complete.     

Investigating the Role of Free-Ranging Wild Boar (Sus scrofa) in the Re-Emergence of Enzootic Pneumonia in Domestic Pig Herds: A Pathological,Prevalence and Risk-Factor Study

Enzootic pneumonia (EP) caused by Mycoplasma hyopneumoniae has a significant economic impact on domestic pig production. A control program carried out from 1999 to 2003 successfully reduced disease occurrence in domestic pigs in Switzerland, but recurrent outbreaks suggested a potential role of free-ranging wild boar (Sus scrofa) as a source of re-infection. Since little is known on the epidemiology of EP in wild boar populations, our aims were: (1) to estimate the prevalence of M. hyopneumoniae infections in wild boar in Switzerland; (2) to identify risk factors for infection in wild boar; and (3) to assess whether infection in wild boar is associated with the same gross and microscopic lesions typical of EP in domestic pigs. Nasal swabs, bronchial swabs and lung samples were collected from 978 wild boar from five study areas in Switzerland between October 2011 and May 2013. Swabs were analyzed by qualitative real time PCR and a histopathological study was conducted on lung tissues. Risk factor analysis was performed using multivariable logistic regression modeling. Overall prevalence in nasal swabs was 26.2% (95% CI 23.3–29.3%) but significant geographical differences were observed. Wild boar density, occurrence of EP outbreaks in domestic pigs and young age were identified as risk factors for infection. There was a significant association between infection and lesions consistent with EP in domestic pigs. We have concluded that M. hyopneumoniae is widespread in the Swiss wild boar population, that the same risk factors for infection of domestic pigs also act as risk factors for infection of wild boar, and that infected wild boar develop lesions similar to those found in domestic pigs. However, based on our data and the outbreak pattern in domestic pigs, we propose that spillover from domestic pigs to wild boar is more likely than transmission from wild boar to pigs.     

BsaH Ⅰ对猪激素敏感脂肪酶基因外显子Ⅰ的PCR-RFLP分析

以华北野猪、东北野猪和山西黑猪、长白猪、大白猪、马身猪共计287头猪作为研究对象,对其HSL基因外显子Ⅰ区域进行了PCR-RFLP多态性研究,发现不同品种猪间存在多态性。瘦肉型大白猪、长白猪全部表现为GG基因型;山西黑猪表现为AA、AG和GG三种基因型;脂肪型地方猪种马身猪为单一的AA基因型;华北杂种野猪、东北纯种野猪及杂种野猪表现为AG和GG两种基因型。等位基因A、G及三种基因型的频率在不同猪种中不同。该研究首次对华北及东北野猪HSL基因进行了多态性研究,丰富了国内外对野猪的分子生物学研究,为野猪遗传资源的合理开发利用提供了依据。     

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.     

Porcine reproductive and respiratory syndrome (PRRS) virus in wild boar and Iberian pigs in south-central Spain

Porcine reproductive and respiratory syndrome (PRRS) is a swine infectious disease causing major economic problems on the intensive pig industry. This virus has been reported worldwide in domestic pigs and there is evidence of PRRS virus (PRRSV) infection in wild boar (Sus scrofa). Nonetheless, the epidemiological role of wild boar and extensively kept domestic pigs remains unclear. The aim of this study was to determine the occurrence of PRRS in wild boar and Iberian pigs in the dehesa ecosystem of the Castile-La Mancha region of Spain, which boasts one of the most important free-roaming porcine livestock and hunting industries in the country. Using geo-spatial analysis of literature data, we first explored the relationship between domestic pig density and PRRS occurrence in wild boar in Europe. Results revealed that PRRS occurrence in wild boar may be influenced, albeit not significantly, by domestic pig density. Next, we analyzed sera from 294 wild boar and 80 Iberian pigs by indirect enzyme-linked immunosorbent assay for PRRSV antibodies. The sera and 27 wild boar tissue samples were analyzed by two real-time RT-PCR assays, targeting the most conserved genes of the PRRSV genome, ORF1 and ORF7. Seven wild boar (2.4 %) and one Iberian pig (1.3 %) were seropositive, while none of the animals tested positive for PRRSV by RT-PCR. Our results confirm the limited spread of PRRSV in free-roaming Iberian pigs and wild boar living in mutual contact. Further studies would be necessary to address whether this low seroprevalence found in these animals reflects transmission from intensively kept pigs or the independent circulation of specific strains in free-roaming pigs.     

Attractants for wild pigs: current use,availability, needs,and future potential

Populations of wild pigs (Sus scrofa) are burgeoning around the globe, and they are currently the target of extensive research and management efforts. Wild pigs are a highly successful invasive species that cause extensive damage to agriculture and native plant and animal communities. Lethal control is the most common management strategy used to reduce wild pig populations and their damage, and many lethal strategies rely on luring wild pigs to a specific location. Most commonly, a food commodity such as corn or maize (Zea mays) is used for attracting wild pigs to a site, but baiting with food is sometimes prohibited under wildlife laws, and visitation can be variable due to availability of alternative foods, level of harassment by humans, and acceptance of novel food source, devices, and activity. Wild pigs are highly adaptable with refined senses that enable them to interact with their environment and conspecifics in a complex manner. Wild and domestic pigs share keen senses, though differences exist due to suppressed stimuli, evolutionary gains and losses, or other factors related to needs for survival and fitness. Wild pigs routinely rely on acute olfaction to locate food, detect predators, and communicate with conspecifics. A pig’s sense of taste is also considered to be refined and more acute than that of humans. An abundance of evaluations regarding various attractants for wild pigs has been conducted over the last several decades; yet, a scarcity of conclusive results on which attractants to use when and where still exists. As such, we undertook a comprehensive review of available information on potential attractants that could be used to aid management strategies of wild pigs such as hunting/shooting, trapping, pharmaceutical delivery, or density estimation. To complete this review, we assimilated and synthesized the most relevant literature, provide recommendations, and identify attractant evaluation needs for the enhancement of the global management of wild pigs.     

Rooting Out Genetic Structure of Invasive Wild Pigs in Texas

Invasive wild pigs (Sus scrofa), also called feral swine or wild hogs, are recognized as among the most destructive invasive species in the world. Throughout the United States, invasive wild pigs have expanded rapidly over the past 40 years with populations now established in 38 states. Of the estimated 6.9 million wild pigs distributed throughout the United States, Texas supports approximately 40% of the population and similarly bears disproportionate ecological and economic costs. Genetic analyses are an effective tool for understanding invasion pathways and tracking dispersal of invasive species such as wild pigs and have been used recently in California and Florida, USA, which have similarly long-established populations and high densities of wild pigs. Our goals were to use molecular approaches to elucidate invasion and migration processes shaping wild pig populations throughout Texas, compare our results with patterns of genetic structure observed in California and Florida, and provide insights for effective management of this invasive species. We used a high-density single nucleotide polymorphism (SNP) array to evaluate population genetic structure. Genetic clusters of wild pigs throughout Texas demonstrate 2 distinct patterns: weakly resolved, spatially dispersed clusters and well-resolved, spatially localized clusters. The disparity in patterns of genetic structure suggests disparate processes are differentially shaping wild pig populations in various localities throughout the state. Our results differed from the patterns of genetic structure observed in California and Florida, which were characterized by localized genetic clusters. These differences suggest distinct biological and perhaps anthropogenic processes are shaping genetic structure in Texas. Further, these disparities demonstrate the need for location-specific management strategies for controlling wild pig populations and mitigating associated ecological and economic costs. © 2021 The Wildlife Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.     

Genetic diversity in wild (Sus scrofa scrofa) and domestic (Sus scrofa domestica) pigs and their hybrids based on polymorphism of a fragment of the D-loop region in the mitochondrial DNA

We examined the variation in mitochondrial DNA by sequencing the D-loop region in wild and domestic (large-white breed) pigs, in hybrids between domestic and wild pigs, and in Monteiro pigs. A D-loop fragment of approximately 330 bp was amplified by PCR. Sequencing of DNA amplicons identified haplotypes previously described as European and Asian types. Monteiro pigs and wild pigs had European haplotypes and domestic pigs had both European and Asian haplotypes.     

Mitochondrial Genetic Variation in Chinese Pigs and Wild Boars

The mitochondrial DNAs (mtDNAs) from 30 pig breeds (29 Chinese native breeds and 1 European breed) and wild boars were investigated for restriction fragment length polymorphisms (RFLPs) to determine the phylogenetic relationships and genetic diversity among pig breeds and wild boars. Of the 24 enzymes used, 8 (AvaI, BclI, BglII, EcoRI, EcoRV, ScaI, StuI, and XbaI) detected polymorphisms. By combining the cleavage patterns for each enzyme, 108 individuals were sorted into eight mtDNA mitotypes. There are two haplotype lineages in domestic pigs, i.e., Chinese and European lineages. The pairwise nucleotide sequence divergence was calculated to be 0.56% between Chinese pigs and European pigs, suggesting that they might have diverged from a common ancestor approximately 280,000 years ago. The wild boars showed more extensive genetic variation, four mitotypes were detected in six wild boars. In addition, one of the Zhejiang wild boars was found to share the same mitotype with Chinese native pigs. A UPGMA tree based on genetic distance among mitotypes indicated that mtDNAs of Chinese pigs and European pigs are clearly divided into two clusters, and Chinese wild boars are more closely related to the Chinese pigs. Our results provide molecular evidence to support the previous hypothesis that pigs may be derived from two maternal origins, Asian and European wild boars. Chinese native pig breeds may have a single origin.     

The origin and genetic differentiation of native breeds of pigs in southwest China: An approach from mitochondrial DNA polymorphism

Mitochondrial DNA (mtDNA) of six breeds of native domestic pigs from Yunnan province, southwest China, and two wild boars obtained from Sichuan, China, and Vietnam was analyzed using 20 restriction endonucleases that recognize six nucleotides. Restriction maps were made by double-digestion methods and polymorphic sites were located on the map. According to their mtDNA restriction types, all the breeds were classified into six groups. Genetic distances among groups were calculated to define their phylogenetic relationships. The relationship between the Sichuan wild boar and domestic pigs is close, while the Vietnamese wild boar is relatively far from them, so the domestic pigs in southwest China are likely to have originated from a wild pig which distributed in west China. We compare our results with previous reports in literature and discuss the relationship among Chinese pigs, Japanese pigs, and European pigs. The mtDNA cleavage pattern of the Mingguang pig digested byEcoRV was identical to that of Duroc; mutations at theEcoRI site, detected in the mtDNA of two Dahe pigs, are the same as in the Vietnamese wild boar, suggesting that mutational hot spots exist in the mtDNA of pigs.     

Fiber types and metabolic characteristics in muscles of wild boars, normal and halothane sensitive Swedish landrace pigs

Muscle fiber characteristics, glycogen content and enzyme activities were studied in muscles of six Swedish landrace pigs, six wild boars and in three halothane sensitive landrace pigs. The wild boars have a higher proportion of type I and IIA fibers compared with Swedish landrace pigs. Fiber composition is similar in landrace pigs and halothane sensitive landrace pigs. The wild boars revealed the highest citrate synthase (CS) and 3-OH-acyl-CoA dehydrogenase (HAD) activities and the lowest glycogen content compared with the other two groups. Lower CS and HAD activities were observed in the halothane sensitive pigs compared with the other pigs. The data show that wild boars have a higher and halothane sensitive landrace pigs a lower aerobic capacity in skeletal muscles compared with Swedish landrace pigs.     

Opportunistic Predation of Wild Turkey Nests by Wild Pigs

Wild pigs (Sus scrofa; i.e., feral hogs, feral swine) are considered an invasive species in the United States. Where they occur, they damage agricultural crops and wildlife habitat. Wild pigs also depredate native wildlife, particularly ground-nesting bird species during nesting season. In areas inhabited by wild turkeys (Meleagris gallopavo), nest destruction caused by wild pigs may affect recruitment. There is debate whether wild pigs actively seek ground-nesting bird nests or depredate them opportunistically. To address this debate, in 2016 we examined the movements of wild pigs relative to artificial wild turkey nests (i.e., control [no artificial nests], moderate density [12.5–25 nests/km²], and high density [25–50 nests/km²]) throughout the nesting season (i.e., early, peak, and late) in south-central Texas, USA. We found no evidence that wild pigs learned to seek and depredate wild turkey nests relative to nest density or nesting periods. Despite wild pigs being important nest predators, depredation was not a functional response to a pulsed food resource and can only be associated with overlapping densities of wild pigs and nests. Protecting reproductive success of wild turkeys will require reducing wild pig densities in nesting habitat prior to nesting season. © 2019 The Wildlife Society.     

TYR基因外显子1的序列变异

为了分析家猪与野猪的遗传多样性及起源,测定了来自１２个中国地方家猪品种、３个欧洲引进猪品种以及8个中国野猪和2个越南野猪共36个个体的酪氨酸酶基因（TYR）外显子1的序列,共检出６个单核苷酸多态性位点（SNPs）,且这6个位点的变异均为同义突变,根据这些变异可将酪氨酸酶基因DNA序列归结为４种单倍型。结合已发表的数据,构建了简约中介网络图。 在网络图中,单倍型TYR*2主要为欧洲家猪与欧洲野猪和三条亚洲家猪染色体。大部分亚洲家猪和野猪共享单倍型TYR*1,表明这是一个亚洲类型的单倍型;同时也有部分欧洲家猪与野猪携带这一单倍型。 而单倍型TYR*3和TYR*4为本研究检测到的稀有单倍型,这两种单倍型主要由中国家猪与亚洲野猪组成。这种网络图结构支持家猪的欧洲和亚洲独立起源学说,同时也表明相当部分的欧洲家猪品种受到亚洲猪的基因渗透,而少量中国家猪和日本野猪也受到了欧洲猪的基因渗透。     

Variation in mitochondrial DNA of Vietnamese pigs: relationships with Asian domestic pigs and Ryukyu wild boars

Mitochondrial DNA (mtDNA) sequences (574 bp) of 30 Vietnamese pigs (large and small) were examined and compared with those of 61 haplotypes from wild boars and domestic pigs from various locations in Asia. The large Vietnamese pigs had genetic links to Ryukyu wild boars in southern Japan. The small Vietnamese pigs were closely related to other East Asian domestic pigs. These results indicate that Vietnamese pigs are genetically diverse and may be descendents of wild and domestic pigs from other regions of Asia.     

Chromosome R-banding patterns and NOR homologies in the European wild pig and four breeds of domestic pig

Four European wild pigs and 27 domestic pigs were studied; three Landrace, 12 village pigs from Papua New Guinea, two Chinese pigs Meishan and 10 Creole pigs from the French Antilles. The R-banding patterns were identical for all domestic breeds despite their different history and geographical divergence. The European wild pigs showed a similar R-banding pattern and a centric fusion between pairs 15 and 17 (2n = 36). The nucleolar organizers (NORs) in the European wild pig and the four domestic breeds were localized on the secondary constriction of chromosomes 8 and 10. All animals exhibited in the majority of metaphases two NORs on both chromosomes 10. In some animals. the NORs were expressed only in one of the homologs of chromosome 8. The Chinese pigs had a high amount of silver precipitates on two homologs of chromosome 8. This study confirms several previous reports on the polymorphism of NOR patterns in different domestic pig breeds.     

Mitochondrial haplotypes of European wild boars with 2n = 36 are closely related to those of European domestic pigs with 2n = 38

Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10-fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.     

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.     

Sanitary Waste Landfill Effects on an Invasive Wild Pig Population

Being opportunistic omnivores, wild pigs (Sus scrofa) readily feed on edible garbage. Given the presence of substantial volumes of edible food waste, large multi-county and regional municipal sanitary waste landfills constitute attractive forage resources for pigs, providing a year-round anthropogenic source of potentially high-quality forage. Our objective was to assess the effects that a large regional landfill has on the local pigs foraging in that facility's waste disposal cells. The landfill, located on the United States Department of Energy's Savannah River Site (SRS) in South Carolina, USA, became operational in 1998 and pigs began foraging there in 2001. By 2009 >100 pigs/night were observed foraging in the landfill, suggesting landfill establishment may have important consequences for population dynamics, public safety, and disease transmission. We evaluated changes in body mass, fetal litter size, numbers of pigs removed, and wild pig-vehicle collisions (WPVCs) before (1980–2000) and after (2001–2019) pigs began foraging in the landfill on SRS. Body mass during the after period increased to a greater extent for pigs in the vicinity of the landfill compared to pigs on the rest of SRS. Fetal litter size increased for pigs in the vicinity of the landfill, whereas it remained unchanged on the rest of SRS. Our density surrogate (number of pigs harvested) increased around the landfill during the after period by 2.9 times, whereas on the rest of the site it only increased by 53%. No WPVCs occurred adjacent to the landfill before 2001, but WPVCs increased along the 2 major roads bordering the landfill after 2001. Effects of sanitary waste landfills on wild pig populations scavenging there can present unique challenges to population management, control, public safety, and disease transmission. Potential approaches to address these challenges could be exclusion fencing to prevent access to the landfill's waste disposal cells or enhanced placement of waste cell covers to reduce access. © 2021 The Wildlife Society.     

Efficiency of time-lapse intervals and simple baits for camera surveys of wild pigs

Growing concerns surrounding established and expanding populations of wild pigs (Sus scrofa) have created the need for rapid and accurate surveys of these populations. We conducted surveys of a portion of the wild pig population on Fort Benning, Georgia, to determine if a longer time-lapse interval than had been previously used in surveys of wild pigs would generate similar detection results. We concurrently examined whether use of soured corn at camera sites affected the time necessary for pigs to locate a new camera site or the time pigs remained at a site. Our results suggest that a 9-min time-lapse interval generated dependable detection results for pigs and that soured corn neither attracted pigs to a site any quicker than plain, dry, whole-kernel corn, nor held them at a site longer. Maximization of time-lapse interval should decrease data and processing loads, and use of a simple, available bait should decrease cost and effort associated with more complicated baits; combination of these concepts should increase efficiency of wild pig surveys. © 2011 The Wildlife Society.     

Multi-locus analysis reveals a different pattern of genetic diversity for mitochondrial and nuclear DNA between wild and domestic pigs in East Asia

Background

A major reduction of genetic diversity in mtDNA occurred during the domestication of East Asian pigs. However, the extent to which genetic diversity has been lost in the nuclear genome is uncertain. To reveal levels and patterns of nucleotide diversity and to elucidate the genetic relationships and demographic history of domestic pigs and their ancestors, wild boars, we investigated 14 nuclear markers (including 8 functional genes, 2 pseudogenes and 4 intergenic regions) from 11 different chromosomes in East Asia-wide samples and pooled them with previously obtained mtDNA data for a combined analysis.

Principal Findings

The results indicated that domestic pigs and wild boars possess comparable levels of nucleotide diversity across the nuclear genome, which is inconsistent with patterns that have been found in mitochondrial genome.

Conclusions

This incongruence between the mtDNA and nuclear genomes is suggestive of a large-scale backcross between male wild boars and female domestic pigs in East Asia. Our data reveal the impacts of founder effects and backcross on the pig genome and help us better understand the complex demographic histories of East Asian pigs, which will be useful for future work on artificial selection.