Mitochondrial lineages reveal intense gene flow between Iberian wild boars and South Iberian pig breeds

The phylogeography of wild boars (WB) and domestic pigs (Sus scrofa) has contributed important insights into where and when domestication occurred. The geographic distribution of two core haplotypes (E1a and E1c) of the main European phylogenetic clade suggests that Central Europe was an early domestication centre, although the complexity of the pattern does not exclude the possibility that multiple domestication events occurred in different regions. To investigate the relationships among WB and domestic pig breeds in Iberia, a fragment of the mitochondrial DNA control region from a large sample (n = 409) of WB and local pig breeds was co‐analysed with published sequences from other European populations. The Iberian sample revealed a high frequency of a sub‐cluster (E1c) of the European haplogroup E1 in 77% of total Iberian samples, 96% of WB, 90% of Alentejano (Portugal) and 87% of Iberian breed pigs (Spain; Black Hairy, Black Hairless and Red varieties). Low genetic distance (F’_ST = 0.105) was observed between Alentejano (Portugal) and Iberian breed pigs (Spain). Alentejano and Iberian breed pigs showed low genetic distances to both Iberian and Central European WB (average F’_ST = 0.345 and 0.215, respectively). This pattern suggests that early pig husbandry in the Iberian Peninsula did not solely rely on imported Central European stock, but also included the recruitment of local WB.     

Testing target‐specific bait delivery for controlling feral pigs in a tropical rainforest

Mitigation of feral pig (Sus scrofa) impacts in Australia’s Wet Tropics World Heritage Area has been impeded by the lack of a target‐specific method for delivering toxic baits in the region. This study evaluated methods to reduce bait‐take by susceptible nontarget species without inhibiting bait‐take by pigs, to enable more effective pig management. We predicted that dingoes would not select an unprocessed corn bait and that other potential nontarget bait consumers would be unable to access the same bait presented under a lightweight cover. Neither of these methods was expected to reduce bait selection or access by pigs. We tested these predictions by monitoring animal interactions with covered and uncovered corn baits, and covered corn and manufactured baits. Use of corn as a bait substrate effectively prevented bait‐take by dingoes. Covering baits substantially reduced bait‐take by other nontarget species and completely prevented nontarget bait‐take when uncovered feed was provided simultaneously. The corn bait preparation was highly acceptable and accessible to feral pigs. We conclude that the methods evaluated here could enable the consideration of poison baiting as a viable method for controlling feral pigs in the World Heritage Area, where it has previously been unavailable.     

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.     

Behavioral states in space and time: understanding landscape use by an invasive mammal

Animal movement models can be used to understand species behavior and assist with implementation of management activities. We explored behavioral states of an invasive wild pig (Sus scrofa) population that recently colonized central Michigan, USA, 2014–2018. To quantify environmental factors related to wild pig movement ecology and spatio-temporal landscape use, we predicted wild pig behavioral states relative to land cover type, landscape structure (i.e., edge and patch cohesion), and weather conditions. We used global positioning system (GPS)-collars and monitored 8 wild pigs from 2014–2018. We fit local convex hulls and calculated movement metrics revealing 3 wild pig behavioral states (resting, exploratory, and relocating) and constructed a 3-level model to predict behavioral state probabilities relative to biotic and abiotic conditions. Probabilities of exploratory and resting behaviors were higher nearer to riparian and open herbaceous cover types (oftentimes emergent marsh), indicating that these cover types provided security cover during activity and bedding. Hard mast cover types had a strong positive association with relocating behaviors. More cohesive patches of agriculture and shrub cover types were associated with higher probabilities of exploratory behaviors, while resting was more likely in continuous patches of agriculture (mostly mid-summer corn). The probability of exploratory behaviors increased exponentially with warming ambient temperature. Our results may be used by managers to develop control strategies conducive to landscape and environmental conditions where the likelihood of encountering wild pigs is highest or targeting wild pigs when in a behavioral state most vulnerable to a particular removal technique.     

Prevalence of Tree Regeneration by Sprouting and Seeding Along a Rainfall Gradient in Hawai'i

Drought stress in tropical dry forests is thought to result in greater asexual regeneration via vegetative sprouting ( e.g ., basal, root, and branch layering) than occurs in moister tropical forests. We tested this hypothesis by examining the prevalence of tree sprouting and seeding in tropical forests located along a rainfall gradient on the island of Hawai'i. Additionally, we examined the potential for novel disturbance, feral pig Sus scrofa rooting and trampling, to alter patterns in tree regeneration mode. We found greater sprouting (in terms of relative density and basal area) in dry forests than in mesic and wet forests, supporting the hypothesis. We also found that feral pig disturbance is negatively correlated with the relative density and basal area of seedlings in wet forests, but is positively correlated with the relative importance of sprouting, and the richness and diversity of sprouting species. Our results suggest rainfall regimes may be an important factor controlling broad-scale patterns in tree regeneration mode, and that exotic ungulates can significantly modify such patterns with potential consequences for the structure and dynamics of tree populations and communities.     

Eradication of Feral Pigs From Pinnacles National Monument

Abstract: Feral pigs (Sus scrofa) have caused considerable damage where they have been introduced around the world. At Pinnacles National Monument, California, USA, managers were concerned that feral pigs were damaging wetland habitats, reducing oak regeneration, competing with native wildlife, and dispersing nonnative plant species through soil disturbance. To address these threats the National Park Service constructed an exclosure around 57 km² of monument land and through cooperation with the Institute for Wildlife Studies eradicated all feral pigs within the area. Trapping, ground-hunting, hunting dogs, and Judas techniques were used to remove feral pigs. Trapping techniques removed most pigs, but a combination of techniques was required to cause eradication. A series of bait sites and transects across the monument helped focus removal efforts and facilitated detection of the last remaining feral pigs in the exclosure. Consistent funding and cooperation from the National Park Service allowed for a seamless and comprehensive program that provided intensive removal of feral pigs. The successful eradication of feral pigs at Pinnacles National Monument should encourage managers in other areas to implement future control or eradication programs.     

Genetic relationship and distribution of the Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (Sus scrofa riukiuanus) analysed by mitochondrial DNA

Mitochondrial genetic variations were used to investigate the relationships between two Japanese wild boars, Japanese wild boar (Sus scrofa leucomystax) and Ryukyu wild boar (S.s. riukiuanus). Nucleotide sequences of the control (27 haplotypes) and cytochrome b (cyt-b) regions (19 haplotypes) were determined from 59 Japanese wild boars, 13 Ryukyu wild boars and 22 other boars and pigs. From phylogenetic analyses, the mtDNA of Ryukyu wild boar has a distinct lineage from that of Japanese wild boar, which was classified into the Asian pig lineage. This result suggests that the Ryukyu wild boar has a separate origin from the Japanese wild boar.     

Mitochondrial DNA Sequence and Phylogenetic Evaluation of Geographically Disparate Sus scrofa Breeds

Next generation sequencing of mitochondrial DNA (mtDNA) facilitates studies into the metabolic characteristics of production animals and their relation to production traits. Sequence analysis of mtDNA from pure-bred swine with highly disparate production characteristics (Mangalica Blonde, Mangalica Swallow-bellied, Meishan, Turopolje, and Yorkshire) was initiated to evaluate the influence of mtDNA polymorphisms on mitochondrial function. Herein, we report the complete mtDNA sequences of five Sus scrofa breeds and evaluate their position within the phylogeny of domestic swine. Phenotypic traits of Yorkshire, Mangalica Blonde, and Swallow-belly swine are presented to demonstrate their metabolic characteristics. Our data support the division of European and Asian breeds noted previously and confirm European ancestry of Mangalica and Turopolje breeds. Furthermore, mtDNA differences between breeds suggest function-altering changes in proteins involved in oxidative phosphorylation such as ATP synthase 6 (MT-ATP6), cytochrome oxidase I (MT-CO1), cytochrome oxidase III (MT-CO3), and cytochrome b (MT-CYB), supporting the hypothesis that mtDNA polymorphisms contribute to differences in metabolic traits between swine breeds. Our sequence data form the basis for future research into the roles of mtDNA in determining production traits in domestic animals. Additionally, such studies should provide insight into how mtDNA haplotype influences the extreme adiposity observed in Mangalica breeds.     

Using a general index approach to analyze camera-trap abundance indices

The lack of variance estimates constrain the utility of abundance indices calculated from camera-trap data. We adapted a General Index model, which allows variance estimation, to analyze camera-trap observations of feral pigs (Sus scrofa) for population monitoring in a tropical rainforest. We tested whether the index would respond to population manipulation, and found that it decreased by 57% following removal of 24 pigs and remained low in the following period. Our method is useful for monitoring other large animals in difficult landscapes, and the model can be used to enhance the value of existing data sets. © 2011 The Wildlife Society.     

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.     

云南保山猪线粒体DNA D-loop区序列初步分析 Primary Analysis of Mitochondrial DNA D-loop Region Sequence in Baoshan Pig

摘要：为了解云南保山猪(Baoshan pig)的遗传多样性及其遗传背景,我们测定了19个个体线粒体DNA D-loop高变区I 15 363～15 801片段序列438 bp。检测到10种单倍型,包括8个多态位点,其中5次T/C转换、1次G/A转换、1次G/C颠换和1次A/T颠换,其A、T、G、C碱基的平均含量分别为35.4%、26.9%、13.2%和24.5%,A+T含量(62.3%)明显高于G+C含量(37.7%)。对于保山猪的保种及其持续利用有着重要的理论指导意义。 Abstract:To investigate the genetic diversity and genetic data of Baoshan pig in Yunnan province,the mitochondrial DNA D-loop hypervariable segment I sequences 15 363～15 801 (438 bp) in 19 individuals of Baoshan pig were sequenced.Ten mitochondrial haplotypes were identified in the samples,with 8 sites showing polymorphism,which were 5 T/C and 1 G/A transitions,1 G/C and 1 A/T transversions.The contents of A,T,G and C were 35.4%,269%,13.2% and 24.5%,respectively.The content of A+T (62.3%) was significantly higher than that of G+C (37.3%).It will be of importance to conservation and sustainable utilization in Baoshan pig.     

贵州省东方蜜蜂Apis cerana线粒体DNA遗传多样性研究

为探明贵州省东方蜜蜂Apis cerana遗传多样性及遗传分化现状,对贵州省9个地级市79个样点采集的东方蜜蜂样本线粒体DNA (mt DNA) COI-COII序列进行扩增与测序,分析其遗传多样性、遗传结构及亲缘关系。序列结果显示扩增后COI-COII序列长度约为760 bp,A+T平均含量（82.3%）明显高于C+G（17.7%）,碱基偏移性明显。单倍型分析共发现33个单倍型,其中主体单倍型H1为9个地理群体共有。单倍型多样度分析表明平均单倍型多样度为0.802,其中黔南地区最高,遵义地区最低;平均核苷酸多样度为0.014,其中六盘水地区最高,黔西南及安顺地区最低。中性检验结果表明贵州省部分地区东方蜜蜂可能经历过群体扩张。9个地区样点的平均遗传距离介于0.0012~0.0044之间,其中毕节与黔东南地区间最大,为0.0044,安顺与黔南、遵义地区间最小,均为0.0012。在单倍型系统进化树中,79个样点东方蜜蜂可分为两个类群。研究结果为贵州省东方蜜蜂遗传分化研究、种质资源保护与开发利用提供参考依据。     

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.     

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.     

广东省地方鸡线粒体遗传多样性与母系起源

系统评估地方鸡的遗传变异水平并追溯其母系起源, 可为保护利用优质家禽种质资源库提供科学依据。本研究测定了广东省和邻省共12个地方鸡品种的线粒体DNA D-loop序列, 分析品种间的遗传距离与系统关系, 并构建单倍型系统发生树和中介网络图。360份样品共检测到60个突变位点, 均为转换。定义了85种单倍型, 归属于单倍型类群A、B、C和E, 在12个鸡品种中均有分布, 其中B是优势单倍型类群(187个, 51.94%), E次之(76个, 21.11%)。B02 和C01是优势单倍型(85个, 23.61%; 48个, 13.33%), 为12个鸡品种共有; E03位居第三(35个, 9.72%), 杏花鸡、黄郎鸡和宁都三黄鸡未见此单倍型。杏花鸡集中分布在单倍型类群B, 惠阳胡须鸡和中山沙栏鸡则主要分布在单倍型类群E; 怀乡鸡的单倍型数量最多, 中山沙栏鸡的最少。广东地方鸡品种间遗传距离为0.012-0.015, 单倍型多样性0.805 ± 0.047至0.949 ± 0.026, 核苷酸多样性0.0102 ± 0.0017至0.0138 ± 0.0009。邻接树和中介网络图将85种单倍型划分为进化枝A、B、C和E, 广东省与邻省地方鸡单倍型的地理分布模式相似。中性检验显示广东地方鸡未经历明显的群体历史扩张。结果表明广东地方鸡处于较好的保护状态, 遗传多样性水平较高, 品种的形成受到邻省和北方家鸡的影响, 东南亚红原鸡对广东地方鸡也有重要的遗传贡献。     

Reproduction in a population of wild pigs (Sus scrofa) subjected to lethal control

The continued range expansion of wild pigs (Sus scrofa) in North America is an increasing cause for concern because of the numerous negative impacts that wild pigs have on ecosystem structure and function. Once populations are established, wild pigs have proven to be extremely difficult to control, and close to impossible to eradicate. If effective control and removal techniques are to be developed, we must determine if wild pig populations respond to reductions in density by increasing reproductive output. This study was designed to examine if reproductive parameters of female wild pigs display a density-dependent response following a concentrated removal effort. We compared reproductive parameters and condition of adult sows that were collected between a control area and a treatment area where lethal removal occurred. From August 2004 to May 2006, we focused a concentrated removal effort within the treatment area. Although the population density was more than 65% greater in the control area than the treatment area during the study, we did not detect differences between areas for condition, litter size, ovarian mass, corpus luteum mass, or corpora lutea number. Several years of heavy mast production during the study may have negated any effect on condition and subsequent reproduction between the 2 study areas. These data suggest that reproductive parameters of wild pigs do not exhibit density-dependence during periods when pig populations are in good condition. © 2012 The Wildlife Society.     

Mitochondrial genome diversity in soybean: repeats and rearrangements

Mitochondrial (mt) genome organization in soybean was examined at the molecular level. This study builds upon previous reports that four soybean cytoplasmic groups, Bedford, Arksoy, Lincoln, and soja-forage, are differentiated by polymorphisms detected with a 2.3 kb Hind III mtDNA probe [12]. The variation detected results from DNA alterations in a region within and around a 4.8 kb repeat. The Bedford-type cytoplasm is the only cytoplasm that contains copies of a 4.8 kb repeat in four different genomic environments, evidence that it is recombinationally active. The Lincoln- and Arksoy-type cytoplasms each contain two copies of the repeat, as well as unique fragments that appear to result from rare recombination events outside, but near, the repeat. The soja-forage-type cytoplasm contains no complete copies of the repeat, but does contain a unique truncated version of the repeat. Sequence analysis indicates that the truncation is a result of recombination across a 9 bp repeated sequence, CCCCTCCCC. The structural rearrangements that have occurred in the region surrounding the 4.8 kb repeat may provide a means to dissect species relationships and evolution within the subgenus soja.