Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations

Hybrids of two destructive subterranean termites established in the field, revealing a potential for gene flow between species

Hybridization between invasive pest species may lead to significant genetic and economic impacts that require close monitoring. The two most invasive and destructive termite species worldwide, Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann), have the potential for hybridization in the field. A three-year field survey conducted during the dispersal flight season of Coptotermes in Taiwan identified alates with atypical morphology, which were confirmed as hybrids of the two Coptotermes species using microsatellite and mitochondrial analyses. Out of 27,601 alates collected over three years, 4.4% were confirmed as hybrid alates, and some advanced hybrids (>F1 generations) were identified. The hybrid alates had a dispersal flight season that overlapped with the two parental species 13 out of 15 times. Most of the hybrid alates were females, implying that mating opportunities beyond F1 may primarily be possible through female hybrids. However, the incipient colony growth results from all potential mating combinations suggest that only backcross colonies with hybrid males could sometimes lead to brood development. The observed asymmetrical viability and fertility of hybrid alates may critically reduce the probability of advanced-hybrid colonies being established in the field.

Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds

Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.

Anthropogenic hybridization and its influence on the adaptive potential of the Sardinian wild boar (Sus scrofa meridionalis)

The wild boar (Sus scrofa meridionalis) arrived in Sardinia with the first human settlers in the early Neolithic with the potential to hybridize with the domestic pig (S. s. domesticus) throughout its evolution on the island. In this paper, we investigated the possible microevolutionary effects of such introgressive hybridization on the present wild boar population, comparing Sardinian wild specimens with several commercial pig breeds and Sardinian local pigs, along with a putatively unadmixed wild boar population from Central Italy, all genotyped with a medium density SNP chip. We first aimed at identifying hybrids in the population using different approaches, then examined genomic regions enriched for domestic alleles in the hybrid group, and finally we applied two methods to find regions under positive selection to possibly highlight instances of domestic adaptive introgression into a wild population. We found three hybrids within the Sardinian sample (3.1% out of the whole dataset). We reported 11 significant windows under positive selection with a method that looks for overly differentiated loci in the target population, compared with other two populations. We also identified 82 genomic regions with signs of selection in the domestic pig but not in the wild boar, two of which overlapped with genomic regions enriched for domestic alleles in the hybrid pool. Genes in these regions can be linked with reproductive success. Given our results, domestic introgression does not seem to be pervasive in the Sardinian wild boar. Nevertheless, we suggest monitoring the possible spread of advantageous domestic alleles in the coming years.

Genome-Wide Re-Sequencing Data Reveals the Population Structure and Selection Signatures of Tunchang Pigs in China

Tunchang pig is one population of Hainan pig in the Hainan Province of China, with the characteristics of delicious meat, strong adaptability, and high resistance to diseases. To explore the genetic diversity and population structure of Tunchang pigs and uncover their germplasm characteristics, 10 unrelated Tunchang pigs were re-sequenced using the Illumina NovaSeq 150 bp paired-end platform with an average depth of 10×. Sequencing data from 36 individuals of 7 other pig breeds (including 4 local Chinese pig breeds (5 Jinhua, 5 Meishan, 5 Rongchang, and 6 Wuzhishan), and 3 commonly used commercial pig breeds (5 Duorc, 5 Landrace, and 5 Large White)) were downloaded from the NCBI public database. After analysis of genetic diversity and population structure, it has been found that compared to commercial pigs, Tunchang pigs have higher genetic diversity and are genetically close to native Chinese breeds. Three methods, FST, θπ, and XP-EHH, were used to detect selection signals for three breeds of pigs: Tunchang, Duroc, and Landrace. A total of 2117 significantly selected regions and 201 candidate genes were screened. Gene enrichment analysis showed that candidate genes were mainly associated with good adaptability, disease resistance, and lipid metabolism traits. Finally, further screening was conducted to identify potential candidate genes related to phenotypic traits, including meat quality (SELENOV, CBR4, TNNT1, TNNT3, VPS13A, PLD3, SRFBP1, and SSPN), immune regulation (CD48, FBL, PTPRH, GNA14, LOX, SLAMF6, CALCOCO1, IRGC, and ZNF667), growth and development (SYT5, PRX, PPP1R12C, and SMG9), reproduction (LGALS13 and EPG5), vision (SLC9A8 and KCNV2), energy metabolism (ATP5G2), cell migration (EPS8L1), and olfaction (GRK3). In summary, our research results provide a genomic overview of the genetic variation, genetic diversity, and population structure of the Tunchang pig population, which will be valuable for breeding and conservation of Tunchang pigs in the future.

Cranial Morphology of Lithuanian Indigenous Wattle Pigs and Their Hybrids with Wild Boar

The diversity of domestic pig breeds and their hybridization increases the variety of phenotypes expressed in hybrids. The aim of this study was to quantify the differences of cranial morphologies between local Lithuanian Indigenous Wattle pigs and theirhybrids with wild boar. A total of sixteen craniometric measurements were performed on the lateral, ventral and dorsal sides of 71 skulls of Lithuanian Indigenous Wattle pigs and their hybrids, including 1/4 wild boar (WB), 1/2 wild boar and 3/4 wild boar genotypes. The weight of the skull was affected by the genotype, live weight and sex of the animal. The size of the skull, particularly related to skull length parameters, increased consistently with the increase of the wild boar proportion in the hybrids. However, the Sus scrofa genotype did not affect the skull height. Clear discrimination was possible between the local Lithuanian breed pigs and their hybrids with different proportions of wild boar and between individual groups of hybrids. The most correct classification was determined on the basis of the overall and length parameters of the crania. This could contribute to better management and utilization of hybrids.

Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history

European wildlife has been subjected to intensifying levels of anthropogenic impact throughout the Holocene, yet the main genetic partitioning of many species is thought to still reflect the late-Pleistocene glacial refugia. We analyzed 26,342 nuclear SNPs of 464 wild boar (Sus scrofa) across the European continent to infer demographic history and reassess the genetic consequences of natural and anthropogenic forces. We found that population fragmentation, inbreeding and recent hybridization with domestic pigs have caused the spatial genetic structure to be heterogeneous at the local scale. Underlying local anthropogenic signatures, we found a deep genetic structure in the form of an arch-shaped cline extending from the Dinaric Alps, via Southeastern Europe and the Baltic states, to Western Europe and, finally, to the genetically diverged Iberian peninsula. These findings indicate that, despite considerable anthropogenic influence, the deeper, natural continental structure is still intact. Regarding the glacial refugia, our findings show a weaker signal than generally assumed, but are nevertheless suggestive of two main recolonization routes, with important roles for Southern France and the Balkans. Our results highlight the importance of applying genomic resources and framing genetic results within a species' demographic history and geographic distribution for a better understanding of the complex mixture of underlying processes.

Introduced, Mixed, and Peripheral: Conservation of Mitochondrial-DNA Lineages in the Wild Boar (Sus scrofa L.) Population in the Urals

Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.

Current Analytical Methods and Research Trends Are Used to Identify Domestic Pig and Wild Boar DNA in Meat and Meat Products

The pig, one of the most important livestock species, is a meaningful source of global meat production. It is necessary, however, to prove whether a food product that a discerning customer selects in a store is actually made from pork or venison, or does not contain it at all. The problem of food authenticity is widespread worldwide, and cases of meat adulteration have accelerated the development of food and the identification methods of feed species. It is worth noting that several different molecular biology techniques can identify a porcine component. However, the precise differentiation between wild boar and a domestic pig in meat products is still challenging. This paper presents the current state of knowledge concerning the species identification of the domestic pig and wild boar DNA in meat and its products.

A 20-SNP Panel as a Tool for Genetic Authentication and Traceability of Pig Breeds

Simple Summary

Given the high economic and qualitative values of local-breed meat products, it is not uncommon that substitution or mislabeling (either fraudulent or accidental) occurs at the market level. Therefore, to protect the interests of both producers and consumers, a reliable traceability tool should be developed. Nowadays, traceability usually relies on physical labeling systems (e.g., ear tags, tattoos, or electronic transponders). These systems do not, however, have good performances when dealing with carcasses or processed meat products. Molecular markers (i.e., based on the DNA sequence) can be a solution, since DNA is easily extracted from a wide variety of animal products and parts, and is not degraded during processing, even at the high temperatures involved. The aim of this study was to identify a small number of DNA mutations for breed-traceability purposes, in particular of the Italian Nero Siciliano pig and its derived products. A small panel of 12 DNA mutations was enough to discriminate Nero Siciliano pigs from other pig breeds and from wild boars.

Abstract

Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabeling. The aim of this study was to identify a small number of SNPs using the Illumina PorcineSNP60 BeadChip for breed traceability, in particular of the Italian Nero Siciliano pig and its derived products. A panel of 12 SNPs was sufficient to discriminate Nero Siciliano pig from cosmopolitan breeds and wild boars. After adding 8 SNPs, the final panel of 20 SNPs allowed us to discriminate all the breeds involved in the study, to correctly assign each individual to its breed, and, moreover, to discriminate Nero Siciliano from first-generation hybrids. Almost all livestock breeds are being genotyped with medium- or high-density SNP panels, providing a large amount of information for many applications. Here, we proposed a method to select a reduced SNP panel to be used for the traceability of pig breeds.

Patterns of genetic variation on wild pig (Sus scrofa) populations over a complete range of the species in Argentina

In Argentina, wild pigs (Sus scrofa) are represented by wild boars and feral pigs. These populations inhabit a wide territory due to natural dispersion and human translocation. Previous studies in other countries have detected crossbreeding between the different morphotypes, even with domestic pigs. This crossing can lead to introgression of improved traits in the wild population, which would increase the invasive potential and, therefore, the damage to native ecosystems. The aim of this work was to obtain the patterns of genetic variability throughout its current distribution in Argentina, in order to elucidate genetic relationships between wild boar and feral pig populations through the molecular marker control region. For this purpose, studies of genetic variability and population structure were carried out using 377 sequences from Argentinian wild pigs. The high values of haplotype and nucleotide diversity (Hd = 0.866 and π = 0.00959) obtained, and the cluster analyses (SAMOVA and BAPS) could indicate mixing between wild pigs and/or with domestic pigs. The star-like shapes observed in the haplotype network and neutral tests (Fu’s Fs and Tajima’s D) are consistent with a recent population expansion, supporting previous reports that indicate crossbreeding increases invasive potential.

Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions

Owing to the intensified domestication process with artificial trait selection, introgressive hybridisation between domestic and wild species poses a management problem. Traditional free-range livestock husbandry, as practiced in Corsica and Sardinia, is known to facilitate hybridisation between wild boars and domestic pigs (Sus scrofa). Here, we assessed the genetic distinctness and genome-wide domestic pig ancestry levels of the Corsican wild boar subspecies S. s. meridionalis, with reference to its Sardinian conspecifics, employing a genome-wide single nucleotide polymorphism (SNP) assay and mitochondrial control region (mtCR) haplotypes. We also assessed the reliance of morphological criteria and the melanocortin-1 receptor (MC1R) coat colour gene to identify individuals with domestic introgression. While Corsican wild boars showed closest affinity to Sardinian and Italian wild boars compared to other European populations based on principal component analysis, the observation of previously undescribed mtCR haplotypes and high levels of nuclear divergence (Weir’s θ > 0.14) highlighted the genetic distinctness of Corsican S. s. meridionalis. Across three complementary analyses of mixed ancestry (i.e., STRUCTURE, PCADMIX, and ELAI), proportions of domestic pig ancestry were estimated at 9.5% in Corsican wild boars, which was significantly higher than in wild boars in Sardinia, where free-range pig keeping was banned in 2012. Comparison of morphologically pure- and hybrid-looking Corsican wild boars suggested a weak correlation between morphological criteria and genome-wide domestic pig ancestry. The study highlights the usefulness of molecular markers to assess the direct impacts of management practices on gene flow between domestic and wild species.

Influence of biotic and abiotic factors on home range size and shape of invasive wild pigs (Sus scrofa)

BACKGROUND

Determining factors influencing animal movements at a temporal scale that is similar to that at which management actions are conducted (e.g. weekly) is crucial for identifying efficient methods of wildlife conservation and management. Using global positioning system (GPS) data from 49 wild pigs in the southeast United States, we constructed weekly 50% and 95% utilization distributions to quantify the effects of biotic and abiotic factors on weekly core area and home range size, as well as home range shape.

RESULTS

We found vegetative composition (i.e. proportion of bottomland hardwoods), season (based on forage availability), meteorological conditions (i.e. temperature and pressure), and sex influenced wild pig weekly home range and core area size, while vegetative composition (i.e. proportion of upland pines) and landscape features (i.e. distance to streams) also were important factors influencing home range shape. At close distances to streams, wild pigs had more elongate home ranges when their home ranges comprised less upland pine habitat; however, farther from streams, there was no change in home range shape across fluctuating proportions of upland pines.

CONCLUSION

These results demonstrate that fine-scale wild pig home ranges and movements are pliable from week to week and influenced by several habitat, landscape, and meteorological attributes that can easily be quantified from available land use and meteorological databases. These findings are important for designing monitoring studies, identifying high risk zones for disease transmission, planning response to disease emergence events, and allowing more effective and efficient short-term management planning.

Resilience to Historical Human Manipulations in the Genomic Variation of Italian Wild Boar Populations

Human activities can globally modify natural ecosystems determining ecological, demographic and range perturbations for several animal species. These changes can jeopardize native gene pools in different ways, leading either to genetic homogenization, or conversely, to the split into genetically divergent demes. In the past decades, most European wild boar (Sus scrofa) populations were heavily managed by humans. Anthropic manipulations have strongly affected also Italian populations through heavy hunting, translocations and reintroductions that might have deeply modified their original gene pools. In this study, exploiting the availability of the well-mapped porcine genome, we applied genomic tools to explore genome-wide variability in Italian wild boar populations, investigate their genetic structure and detect signatures of possible introgression from domestic pigs and non-native wild boar. Genomic data from 134 wild boar sampled in six areas of peninsular Italy and in Sardinia were gathered using the Illumina Porcine SNP60 BeadChip (60k Single Nucleotide Polymorphisms – SNPs) and compared with reference genotypes from European specimens and from domestic pigs (both commercial and Italian local breeds), using multivariate and maximum-likelihood approaches. Pairwise FST values, multivariate analysis and assignment procedures indicated that Italian populations were highly differentiated from all the other analyzed European wild boar populations. Overall, a lower heterozygosity was found in the Italian population than in the other European regions. The most diverging populations in Castelporziano Presidential Estate and Maremma Regional Park can be the result of long-lasting isolation, reduced population size and genetic drift. Conversely, an unexpected similarity was found among Apennine populations, even at high distances. Signatures of introgression from both non-Italian wild boar and domestic breeds were very limited. To summarize, we successfully applied genome-wide procedures to explore, for the first time, the genomic diversity of Italian wild boar, demonstrating that they represent a strongly heterogeneous assemblage of demes with different demographic and manipulation histories. Nonetheless, our results suggest that a native component of genomic variation is predominant over exogenous ones in most populations.

Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar

The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935-1988, 7705 boars were caught in various regions of the European part of Russia, the Far East, Ukraine, Belarus, Kyrgyzstan, Kazakhstan, Latvia, Lithuania, Estonia, Tajikistan and resettled in the territory of Russia. Asian and European wild boars dwell the territory of Russia. The aim of our research was to study the genetic diversity and structure of wild boar populations in different regions of Russia using genome-wide genotyping. We have determined the genetic distances, population structure, parameters of genetic diversity and significantly expanded our understanding of the genetic state of the Russian wild boar. For the first time, we calculated autozygosity of the wild boar of the European and Asian subspecies using Homozygous-by-Descent (HBD) Segments analysis, which is important in terms of population recovery. We also found evidence of hybridization between Russian wild boar and domestic pigs. A group of European wild boars showed introgression of the Asian boar into population. The mean level of the inbreeding coefficient in European wild boar was higher than in Asian wild boar, and combined groups of the European boar had higher inbreeding coefficient than Russian wild boars. These results obtained can be used in population management.

Identification of Mammalian and Poultry Species in Food and Pet Food Samples Using 16S rDNA Metabarcoding

The substitution of more appreciated animal species by animal species of lower commercial value is a common type of meat product adulteration. DNA metabarcoding, the combination of DNA barcoding with next-generation sequencing (NGS), plays an increasing role in food authentication. In the present study, we investigated the applicability of a DNA metabarcoding method for routine analysis of mammalian and poultry species in food and pet food products. We analyzed a total of 104 samples (25 reference samples, 56 food products and 23 pet food products) by DNA metabarcoding and by using a commercial DNA array and/or by real-time PCR. The qualitative and quantitative results obtained by the DNA metabarcoding method were in line with those obtained by PCR. Results from the independent analysis of a subset of seven reference samples in two laboratories demonstrate the robustness and reproducibility of the DNA metabarcoding method. DNA metabarcoding is particularly suitable for detecting unexpected species ignored by targeted methods such as real-time PCR and can also be an attractive alternative with respect to the expenses as indicated by current data from the cost accounting of the AGES laboratory. Our results for the commercial samples show that in addition to food products, DNA metabarcoding is particularly applicable to pet food products, which frequently contain multiple animal species and are also highly prone to adulteration as indicated by the high portion of analyzed pet food products containing undeclared species.

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa-Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa-Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.

Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima

Natural and anthropogenic disasters have the capability to cause sudden extrinsic environmental changes and long-lasting perturbations including invasive species, species expansion and influence evolution as selective pressures force adaption. Such disasters occurred on 11 March 2011, in Fukushima, Japan, when an earthquake, tsunami and meltdown of a nuclear power plant all drastically reformed anthropogenic land use. Using genetic data, we demonstrate how wild boar (Sus scrofa leucomystax) have persevered against these environmental changes, including an invasion of escaped domestic pigs (Sus scrofa domesticus). Concurrently, we show evidence of successful hybridization between pigs and native wild boar in this area; however in future offspring, the pig legacy has been diluted through time. We speculate that the range expansion dynamics inhibit long-term introgression and introgressed alleles will continue to decrease at each generation while only maternally inherited organelles will persist. Using the gene flow data among wild boar, we assume that offspring from hybrid lineages will continue dispersal north at low frequencies as climates warm. We conclude that future risks for wild boar in this area include intraspecies competition, revitalization of human-related disruptions and disease outbreaks.

Genomic Analysis Reveals Human-Mediated Introgression From European Commercial Pigs to Henan Indigenous Pigs

Introgression of genetic features from European pigs into Chinese pigs was reported possibly contributing to improvements in productivity traits, such as feed conversion efficiency and body size. However, the genomic differences from European pigs and the potential role of introgression in Henan indigenous pigs remains unclear. In this study, we found significant introgression from European pigs into the genome of Chinese indigenous pigs, especially in Henan indigenous pigs. The introgression in Henan indigenous pigs, particularly in the Nanyang black pig, was mainly derived from Duroc pigs. Most importantly, we found that the NR6A1, GPD2, and CSRNP3 genes were introgressed and reshaped by artificial selection, and these may have contributed to increases in pig body size and feed conversion efficiency. Our results suggest that human-mediated introgression and selection have reshaped the genome of Henan pigs and improved several of their desired traits. These findings contribute to our understanding of the history of Henan indigenous pigs and provide insights into the genetic mechanisms affecting economically important traits in pig populations.

Insight into the Genetic Population Structure of Wild Red Foxes in Poland Reveals Low Risk of Genetic Introgression from Escaped Farm Red Foxes

In this study we assessed the level of genetic introgression between red foxes bred on fur farms in Poland and the native wild population. We also evaluated the impact of a geographic barrier and isolation by distance on gene flow between two isolated subpopulations of the native red fox and their genetic differentiation. Nuclear and mitochondrial DNA was collected from a total of 308 individuals (200 farm and 108 wild red foxes) to study non-native allele flow from farm into wild red fox populations. Genetic structure analyses performed using 24 autosomal microsatellites showed two genetic clusters as being the most probable number of distinct populations. No strong admixture signals between farm and wild red foxes were detected, and significant genetic differentiation was identified between the two groups. This was also apparent from the mtDNA analysis. None of the concatenated haplotypes detected in farm foxes was found in wild animals. The consequence of this was that the haplotype network displayed two genetically distinct groups: farm foxes were completely separated from native ones. Neither the River Vistula nor isolation by distance had a significant impact on gene flow between the separated wild red fox subpopulations. The results of our research indicate a low probability of genetic introgression between farm and native red foxes, and no threat to the genetic integrity of this species.

Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China

Simple Summary

The wild boar is native to the temperate region of Eurasia, which is now one of the most widely distributed mammals worldwide. The recent expansion in the wild boar population has attracted a lot of attention, which may cause great damage to ecosystems. Elucidating the patterns of the population structure, genetic diversity, population origin, and colonization route of wild boar is very helpful in the conservation and management of wild populations. Phylogeographic analysis has proven to be a powerful tool. Here, 82 samples of wild boars in 16 sampling locations were collected in Qinling Mountains (QM). Genetic analysis was conducted based on the mitochondrial control region and nuclear genes. The level of genetic diversity of wild boars in QM was lower than the total population in East Asia, but higher than European population. No obvious phylogeographic pattern were found. The effective population size was under demographic equilibrium in the past.

Abstract

Species dispersal patterns and population genetic structure can be influenced by geographical features. Qinling Mountains (QM) provide an excellent area for phylogeographic study. The phylogeography of Asian-wide wild boars revealed the colonization route. However, the impact of the QM on genetic diversity, genetic structure and population origin is still poorly understood. In this study, genetic analysis of wild boar in the QM was conducted based on the mitochondrial control region (943 bp) and twelve microsatellite loci of 82 individuals in 16 sampling locations. Overall genetic haplotype diversity was 0.86, and the nucleotide diversity was 0.0079. A total of 17 new haplotypes were detected. The level of genetic diversity of wild boars in QM was lower than in East Asia, but higher than in Europe. Phylogenetic analysis showed the weak genetic divergence in QM. Mismatch analysis, neutrality tests, and Bayesian Skyline Plot (BSP) results revealed that the estimates of effective population size were under demographic equilibrium in the past. Spatial analysis of molecular variance indicated no obvious phylogeographic structure.

Applicability of a duplex and four singleplex real-time PCR assays for the qualitative and quantitative determination of wild boar and domestic pig meat in processed food products

Appropriate analytical methods are needed for the detection of food authentication. We investigated the applicability of a duplex real-time PCR assay targeting chromosome 1 and two singleplex real-time PCR assays targeting chromosome 9, both published recently, for the qualitative and quantitative determination of wild boar and domestic pig in processed food products. In addition, two singleplex real-time PCR assays targeting chromosome 7 were tested for their suitability to differentiate the two subspecies. Even by targeting the three genome loci, the probability of misclassification was not completely eliminated. Application of the real-time PCR assays to a total of 35 commercial meat products, including 22 goulash products, revealed that domestic pig DNA was frequently present, even in 14 out of 15 products declared to consist of 100% wild boar. Quantitative results obtained with the real-time PCR assays for wild boar (p < 0.001) and those for domestic pig (p < 0.001) were significantly different. However, the results obtained with the real-time PCR assays for wild boar (r = 0.673; p < 0.001) and those for domestic pig (r = 0.505; p = 0.002) were found to be significantly correlated. If the rules given in the paper are followed, the real-time PCR assays are applicable for routine analysis.

Spatial genetic structure and historical demography of East Asian wild boar

Pleistocene climatic fluctuations may have had a profound impact on the evolutionary history of many species. The geographical pattern of European wild boar (Sus scrofa) is clearly studied, and it was greatly influenced by ancient climatic events, especially the Last Glacial Maximum. Previous research on genetic variation has mainly focused on the origin and distribution histories of domestic pigs. However, some questions have not been answered, including those concerning the genetic diversity, geographical pattern and possible historic influence of climate on East Asian wild boar (EAWB). Employing the control region of mtDNA (511 bp), we investigated the contributions of historic climate, which possibly shaped the genetic pattern of wild boar. Given that the level of genetic diversity of wild boars is higher in East Asia than in Europe, 172 haplotypes were detected from 680 individuals. Phylogenetic analysis demonstrated the complex phylogeographic structure of EAWB. Mismatch analysis, neutrality tests and the Bayesian Skyline Plot results all retrieved signals of a rapid population expansion, which might have played an important role in driving the formation of complex spatial genetic structure. Genetic data and species distribution modelling showed that the Last Glacial Maximum had weak effect on the distribution of the EAWB. We suggest that, in shaping spatial genetic structure in East Asian, long-term gene flow and population history played more important roles than Pleistocene climate fluctuations.

Conservation Genomic Analysis of the Croatian Indigenous Black Slavonian and Turopolje Pig Breeds

The majority of the nearly 400 existing local pig breeds are adapted to specific environments and human needs. The demand for large production quantities and the industrialized pig production have caused a rapid decline of many local pig breeds in recent decades. Black Slavonian pig and Turopolje pig, the latter highly threatened, are the two Croatian local indigenous breeds typically grown in extensive or semi-intensive systems. In order to guide a long-term breeding program to prevent the disappearance of these breeds, we analyzed their genetic diversity, inbreeding level and relationship with other local breeds across the world, as well as modern breeds and several wild populations, using high throughput genomic data obtained using the Illumina Infinium PorcineSNP60 v2 BeadChip. Multidimensional scaling analysis positioned Black Slavonian pigs close to the UK/North American breeds, while the Turopolje pig clustered within the Mediterranean breeds. Turopolje pig showed a very high inbreeding level (F_ROH>4Mb = 0.400 and F_ROH>8Mb = 0.332) that considerably exceeded the level of full-sib mating, while Black Slavonian pig showed much lower inbreeding (F_ROH>4Mb = 0.098 and F_ROH>8Mb = 0.074), indicating a planned mating strategy. In Croatian local breeds we identified several genome regions showing adaptive selection signals that were not present in commercial breeds. The results obtained in this study reflect the current genetic status and breeding management of the two Croatian indigenous local breeds. Given the small populations of both breeds, a controlled management activity has been implemented in Black Slavonian pigs since their commercial value has been recognized. In contrast, the extremely high inbreeding level observed in Turopolje pig argues for an urgent conservation plan with a long-term, diversity-oriented breeding program.

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.

Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds

Genetic variations introduced via introgression from Western to Chinese pigs have contributed to the performance of Chinese breeds in traits such as growth rate and feed conversion efficiency. However, little is known about the underlying genomic changes that occurred during introgression and the types of traits affected by introgression. To address these questions, 525 animals were characterized using an SNP array to detect genomic regions that had been introgressed from European to indigenous Chinese breeds. The functions of genes located in introgressed regions were also investigated. Our data show that five out of six indigenous Chinese breeds show evidence of introgression from Western pigs, and eight introgressed genome regions are shared by five of the Chinese breeds. A region located on chr13: 12.8-13.1 M was affected by both introgression and artificial selection, and this region contains the glucose absorption related gene, OXSM, and the sensory related gene, NGLY. The results provide a foundation for understanding introgression from Western to indigenous Chinese pigs.

Matching STR and SNP genotyping to discriminate between wild boar, domestic pigs and their recent hybrids for forensic purposes

The genetic discrimination between phylogenetically close taxa can be challenging if their gene pools are not differentiated and there are many shared polymorphisms. The gene flow between wild boar (Sus scrofa) and domestic pig (S. s. domesticus) has never been interrupted from domestication onwards, due to non-stop natural and human-mediated crossbreeding. To date there are no individual genetic markers that are able to distinguish between the two forms, nor even to identify effectively their hybrids. We developed a combined molecular protocol based on multiplex porcine-specific STR-profiling system and new real time PCR-based assays of single polymorphisms in the NR6A1 and MC1R genes to gain high diagnostic power in the differentiation of wild boar, pig and hybrids for forensic purposes. The combined approach correctly assigned individuals to one or the other parental gene pool and identified admixed genotypes. Evidence was found for substantial reduction of false negative results by using multiple marker systems jointly, compared to their use individually. Our protocol is a powerful and cost-effective diagnostic tool that can easily be adopted by most forensic laboratories to assist authorities contrast food adulteration, assure veterinary public health and fight against wildlife crimes, like poaching and illegal detention of wild animals.

Range-wide patterns of human-mediated hybridisation in European wildcats

Hybridisation between wild taxa and their domestic congeners is a significant conservation issue. Domestic species frequently outnumber their wild relatives in population size and distribution and may therefore genetically swamp the native species. The European wildcat (Felis silvestris) has been shown to hybridise with domestic cats (Felis catus). Previously suggested spatially divergent introgression levels have not been confirmed on a European scale due to significant differences in the applied methods to assess hybridisation of the European wildcat. We analysed 926 Felis spp. samples from 13 European countries, using a set of 86 selected ancestry-informative SNPs, 14 microsatellites, and ten mitochondrial and Y-chromosome markers to study regional hybridisation and introgression patterns and population differentiation. We detected 51 hybrids (four F1 and 47 F2 or backcrosses) and 521 pure wildcats throughout Europe. The abundance of hybrids varied considerably among studied populations. All samples from Scotland were identified as F2 hybrids or backcrosses, supporting previous findings that the genetic integrity of that wildcat population has been seriously compromised. In other European populations, low to moderate levels of hybridisation were found, with the lowest levels being in Central and Southeast Europe. The occurrence of distinct maternal and paternal markers between wildcat and domestic cat suggests that there were no severe hybridisation episodes in the past. The overall low (< 1%) prevalence of F1 hybrids suggests a low risk of hybridisation for the long-term genetic integrity of the wildcat in most of Europe. However, regionally elevated introgression rates confirm that hybridisation poses a potential threat. We propose regional in-depth monitoring of hybridisation rates to identify factors driving hybridisation so as to develop effective strategies for conservation.

Was the Cinta Senese Pig Already a Luxury Food in the Late Middle Ages? Ancient DNA and Archaeozoological Evidence from Central Italy

The Cinta senese is a pig breed, highly esteemed for its meat and derived products, characterized by a black coat with a typical white “belt” and documented by scant iconography, since the 13^th–14^th century in Italy. A piece of pottery showing a Cinta pig was found in the Graffignano castle (Northern Latium, Italy) dated 15th–16th centuries, spurring us to investigate the diet of the inhabitants. Ancient DNA analysis was carried out on 21 pig specimens on three nuclear SNPs: (1) g.43597545C>T, on the KIT gene, informative for the identification of the Cinta senese breed; (2) rs81460129, on an intergenic region in chr. 16, which discriminates between domestic pigs and wild boars, and; (3) a SNP on the ZFY/ZFX homologous genes, to determine the sex of the individuals. Our results indicate that the Cinta senese was present in Northern Latium in Late Medieval time, although it was not the only breed, and that pigs, including Cinta, interbred with wild boars, suggesting free-range breeding for all types of pigs. Moreover, the unexpected high proportion of young females may be considered as evidence for the wealth of the family inhabiting the castle.

The footprint of recent and strong demographic decline in the genomes of Mangalitza pigs

The Mangalitza pig breed has suffered strong population reductions due to competition with more productive cosmopolitan breeds. In the current work, we aimed to investigate the effects of this sustained demographic recession on the genomic diversity of Mangalitza pigs. By using the Porcine Single Nucleotid Polymorphism BeadChip, we have characterized the genome-wide diversity of 350 individuals including 45 Red Mangalitza (number of samples; n=20 from Hungary and n=25 from Romania), 37 Blond Mangalitza, 26 Swallow-belly Mangalitza, 48 Blond Mangalitza × Duroc crossbreds, 5 Bazna swine, 143 pigs from the Hampshire, Duroc, Landrace, Large White and Pietrain breeds and 46 wild boars from Romania (n=18) and Hungary (n=28). Performance of a multidimensional scaling plot showed that Landrace, Large White and Pietrain pigs clustered independently from Mangalitza pigs and Romanian and Hungarian wild boars. The number and total length of ROH (runs of homozygosity), as well as FROH coefficients (proportion of the autosomal genome covered ROH) did not show major differences between Mangalitza pigs and other wild and domestic pig populations. However, Romanian and Hungarian Red Mangalitza pigs displayed an increased frequency of very long ROH (>30 Mb) when compared with other porcine breeds. These results indicate that Red Mangalitza pigs underwent recent and strong inbreeding probably as a consequence of severe reductions in census size.

Current status and future recommendations for feral swine disease surveillance in the United States

USDA APHIS Wildlife Services (WS) responded to the threat of feral swine as a pathogen reservoir as early as 2004. To increase awareness and knowledge on that risk, WS began opportunistic sampling of animals harvested by its operational component to curtail swine damage to agriculture and property. Initially, pseudorabies and swine brucellosis were of most concern, as both serve as a potential threat to the domestic swine industry and the latter also possesses zoonotic implications. In 2006, classical swine fever, a foreign animal disease, became the main driver for feral swine pathogen surveillance. Subsequent years of surveillance identified numerous other disease risks inherent within populations of feral swine. Presently, feral swine surveillance falls under the purview of the APHIS National Feral Swine Damage Management Program, which began in 2014. In January 2018, a panel of animal disease experts representing industry, government, and academia were invited to Fort Collins, Colorado to discuss successes of this surveillance, identify any shortcomings or needs, and propose future feral swine surveillance. This manuscript serves to synthesize WS' surveillance and the future direction of these efforts.

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that domestic pigs arrived in Europe, alongside farmers from the Near East ∼8,500 y ago, yet mitochondrial genomes of modern European pigs are derived from European wild boars. To address this conundrum, we obtained mitochondrial and nuclear data from modern and ancient Near Eastern and European pigs. Our analyses indicate that, aside from a coat color gene, most Near Eastern ancestry in the genomes of European domestic pigs disappeared over 3,000 y as a result of interbreeding with local wild boars. This implies that pigs were not domesticated independently in Europe, yet the first 2,500 y of human-mediated selection applied by Near Eastern Neolithic farmers played little role in the development of modern European pigs.

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigs were not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.

Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations

The survival of indigenous European wildcat (Felis silvestris silvestris) populations can be locally threatened by introgressive hybridization with free-ranging domestic cats. Identifying pure wildcats and investigating the ancestry of admixed individuals becomes thus a conservation priority. We analyzed 63k cat Single Nucleotide Polymorphisms (SNPs) with multivariate, Bayesian and gene-search tools to better evaluate admixture levels between domestic and wild cats collected in Europe, timing and ancestry proportions of their hybrids and backcrosses, and track the origin (wild or domestic) of the genomic blocks carried by admixed cats, also looking for possible deviations from neutrality in their inheritance patterns. Small domestic ancestry blocks were detected in the genomes of most admixed cats, which likely originated from hybridization events occurring from 6 to 22 generations in the past. We identified about 1,900 outlier coding genes with excess of wild or domestic ancestry compared to random expectations in the admixed individuals. More than 600 outlier genes were significantly enriched for Gene Ontology (GO) categories mainly related to social behavior, functional and metabolic adaptive processes (wild-like genes), involved in cognition and neural crest development (domestic-like genes), or associated with immune system functions and lipid metabolism (parental-like genes). These kinds of genomic ancestry analyses could be reliably applied to unravel the admixture dynamics in European wildcats, as well as in other hybridizing populations, in order to design more efficient conservation plans.

Mating of escaped domestic pigs with wild boar and possibility of their offspring migration after the Fukushima Daiichi Nuclear Power Plant accident

The 2011 Tohoku earthquake drastically changed human activities in some regions of Fukushima Prefecture, Japan. The subsequent tsunami damage and radioactive pollution from the Fukushima Daiichi nuclear power plant resulted in the evacuation of humans, and abandonment of agricultural lands, allowing population expansion of wildlife into areas formally inhabited by domesticated livestock. Unintentional escape of domesticated pigs into wildlife inhabited environments also occurred. In this study, we tested the possibility of introgression between wild boar and domesticated pigs in Fukushima and neighboring prefectures. We analyzed mitochondrial DNA sequences of 338 wild boar collected from populations in the Tohoku region between 2006 and 2018. Although most boar exhibited Asian boar mitochondrial haplotypes, 18 boar, phenotypically identified as wild boar, had a European domesticated pig haplotype. Frequencies of this haplotype have remained stable since first detection in 2015. This result infers ongoing genetic pollution in wild boar populations from released domesticated pigs. In 2018, this haplotype was detected outside of evacuated areas, suggesting migration and successful adaptation. The natural and anthropocentric disasters at Fukushima gave us the rare opportunity to study introgression processes of domestic genes into populations of wild boar. The present findings suggest a need for additional genetic monitoring to document the dispersal of domestic genes within wild boar stock.

Differentiation between wild boar and domestic pig in food by targeting two gene loci by real-time PCR

Studies indicate that many meat products are not authentic, most frequently because the meat species differ from those given on the food labels. At present, DNA based methods play the most important role in meat species authentication. Discrimination of wild boar and domestic pig meat in food is challenging because it is differentiation on the subspecies level. We developed and validated two singleplex real-time PCR assays targeting SNP rs81416363 on chromosome 9 and a duplex real-time PCR assay targeting SNP g.299084751 C > T in the NR6A1 gene located on chromosome 1. The singleplex real-time PCR assays led to some ambiguous results for Mangalica and Krškopolje pig breeds and wild boar individuals from Germany, the duplex real-time PCR assay particularly for the Turopolje pig breed. We demonstrate that the probability of misclassification can be substantially reduced if the results of both the singleplex real-time PCR assays and the duplex real-time PCR assay are taken into consideration. 86 (91.5%) of a total of 94 individuals, comprising 64 domestic pigs (14 different breeds and 6 cross-breeds) and 30 wild boars (from Austria, Germany, Romania, USA and Estonia), were classified correctly.

Evaluating Cost-Effective Methods for Rapid and Repeatable National Scale Detection and Mapping of Invasive Species Spread

Invasive species can spread rapidly at local and national scales, creating significant environmental and economic impacts. A central problem in mitigation efforts is identifying methods that can rapidly detect invasive species in a cost-effective and repeatable manner. This challenge is particularly acute for species that can spread over large areas (>1 million km²). Wild pigs (Sus scrofa) are one of the most prolific invasive mammals on Earth and cause extensive damage to agricultural crops, native ecosystems, and livestock, and are reservoirs of disease. They have spread from their native range in Eurasia and North Africa into large areas of Australia, Africa, South America, and North America. We show that the range of invasive wild pigs has increased exponentially in Canada over the last 27 years following initial and ongoing releases and escapes from domestic wild boar farms. The cumulative range of wild pigs across Canada is 777,783 km², with the majority of wild pig distribution occurring in the Prairie Provinces. We evaluate eight different data collection and evaluation/validation methods for mapping invasive species over large areas, and assess their benefits and limitations. Our findings effectively map the spread of a highly invasive large mammal and demonstrate that management efforts should ideally rely on a set of complementary independent monitoring methods. Mapping and evaluating resulting species occurrences provide baseline maps against which future changes can be rapidly evaluated.

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 (Krškopolje 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.

Introgression of Chinese haplotypes contributed to the improvement of Danish Duroc pigs

The distribution of Asian ancestry in the genome of Danish Duroc pigs was investigated using whole-genome sequencing data from European wild boars, Danish Duroc, Chinese Meishan and Bamaxiang pigs. Asian haplotypes deriving from Meishan and Bamaxiang occur widely across the genome. Signatures of selection on Asian haplotypes are common in the genome, but few of these haplotypes have been fixed. By defining 50-kb windows with more than 50% Chinese ancestry, which did not exhibit extreme genetic differentiation between Meishan and Bamaxiang as candidate regions, the enrichment of quantitative trait loci in candidate regions supports that Asian haplotypes under selection play an important role in contributing genetic variation underlying production, reproduction, meat and carcass, and exterior traits. Gene annotation of regions with the highest proportion of Chinese ancestry revealed genes of biological interest, such as NR6A1. Further haplotype clustering analysis suggested that a haplotype of Chinese origin around the NR6A1 gene was introduced to Europe and then underwent a selective sweep in European pigs. Besides, functional genes in candidate regions, such as AHR and PGRMC2, associated with fertility, and SAL1, associated with meat quality, were identified. Our results demonstrate the contribution of Asian haplotypes to the genomes of European pigs. Findings herein facilitate further genomic studies such as genomewide association study and genomic prediction by providing ancestry information of variants.

Hotspots of recent hybridization between pigs and wild boars in Europe

After a strong demographic decline before World War II, wild boar populations are expanding and the species is now the second-most abundant ungulate in Europe. This increase raises concerns due to wild boar impact on crops and natural ecosystems and as potential vector of diseases. Additionally, wild boar can hybridize with domestic pigs, which could increase health risks and alter wild boar adaptive potential. We analysed 47,148 Single Nucleotide Polymorphisms in wild boar from Europe (292) and the Near East (16), and commercial (44) and local (255) pig breeds, to discern patterns of hybridization across Europe. We identified 33 wild boars with more than 10% domestic ancestry in their genome, mostly concentrated in Austria, Bosnia and Herzegovina, Bulgaria and Serbia. This difference is probably due to contrasting practices, with free-ranging vs. industrial farming but more samples would be needed to investigate larger geographic patterns. Our results suggest hybridization has occurred over a long period and is still ongoing, as we observed recent hybrids. Although wild and domestic populations have maintained their genetic distinctiveness, potential health threats raise concerns and require implementation of management actions and farming practices aimed at reducing contact between wild and domestic pigs.

Use of molecular data in zoo and aquarium collection management: Benefits, challenges, and best practices

The global zoo and aquarium community widely recognizes that its animal collections and cooperative breeding programs are facing a sustainability crisis. It has become commonly accepted that numerous priority species cannot be maintained unless new management strategies are adopted. While molecular data have the potential to greatly improve management across a range of scenarios, they have been generally underutilized by the zoo and aquarium community. This failure to effectively apply molecular data to collection management has been due, in part, to a paucity of resources within the community on which to base informed decisions about when the use of such data is appropriate and what steps are necessary to successfully integrate data into management. Here, we identify three broad areas of inquiry where molecular data can inform management: 1) taxonomic identification; 2) incomplete or unknown pedigrees; and 3) hereditary disease. Across these topics, we offer a discussion of the advantages, limitations, and considerations for applying molecular data to ex situ animal populations in a style accessible to zoo and aquarium professionals. Ultimately, we intend for this compiled information to serve as a resource for the community to help ensure that molecular projects directly and effectively benefit the long-term persistence of ex situ populations.

A Review of Classical Swine Fever Virus and Routes of Introduction into the United States and the Potential for Virus Establishment

Classical swine fever (CSF) is caused by CSF virus (CSFV) which can be the source of substantial morbidity and mortality events in affected swine. The disease can take one of several forms (acute, chronic, or prenatal) and depending on the virulence of the inoculating strain may result in a lethal infection irrespective of the form acquired. Because of the disease-free status of the United States and the high cost of a viral incursion, a summary of US vulnerabilities for viral introduction and persistence is provided. The legal importation of live animals as well as animal products, byproducts, and animal feed serve as a potential route of viral introduction. Current import regulations are described as are mitigation strategies that are commonly utilized to prevent pathogens, including CSFV, from entering the US. The illegal movement of suids and their products as well as an event of bioterrorism are both feasible routes of viral introduction but are difficult to restrict or regulate. Ultimately, recommendations are made for data that would be useful in the event of a viral incursion. Population and density mapping for feral swine across the United States would be valuable in the event of a viral introduction or spillover; density data could further contribute to understanding the risk of infection in domestic swine. Additionally, ecological and behavioral studies, including those that evaluate the effects of anthropogenic food sources that support feral swine densities far above the carrying capacity would provide invaluable insight to our understanding of how human interventions affect feral swine populations. Further analyses to determine the sampling strategies necessary to detect low levels of antibody prevalence in feral swine would also be valuable.

Genome-wide associations identify novel candidate loci associated with genetic susceptibility to tuberculosis in wild boar

Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized using a high-density single nucleotide polymorphism (SNP) array, while host TB phenotype was assessed using both gross pathology and mycobacterial culture. Two complementary genome-wide association (GWAS) analyses were conducted: (i) infected-uninfected; and (ii) 2002/06–2009/12. The SNPs with the highest allelic frequency differences between time-periods and TB outcomes were identified and validated in a large dataset. In addition, we quantified the expression levels of some of their closest genes. These analyses highlighted various SNPs (i.e. rs81465339, rs81394585, rs81423166) and some of the closest genes (i.e. LOC102164072, BDNF/NT-3, NTRK2, CDH8, IGSF21) as candidates for host genetic susceptibility. In addition to TB-driven selection, our findings outline the putative role of demographic events in shaping genomic variation in natural populations and how population crashes and drift may impact host genetic susceptibility to TB over time.

Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free‐ranging exotic ungulate in the United States. Large and ever‐increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.

Genome-wide association study reveals genetic loci and candidate genes for average daily gain in Duroc pigs

Objective

Average daily gain (ADG) is an important target trait of pig breeding programs. We aimed to identify single nucleotide polymorphisms (SNPs) and genomic regions that are associated with ADG in the Duroc pig population.

Methods

We performed a genome-wide association study involving 390 Duroc boars and by using the PorcineSNP60K Beadchip and two linear models.

Results

After quality control, we detected 3,5971 SNPs, which included seven SNPs that are significantly associated with the ADG of pigs. We identified six quantitative trait loci (QTL) regions for ADG. These QTLs included four previously reported QTLs on Sus scrofa chromosome (SSC) 1, SSC5, SSC9, and SSC13, as well as two novel QTLs on SSC6 and SSC16. In addition, we selected six candidate genes (general transcription factor 3C polypeptide 5, high mobility group AT-hook 2, nicotinamide phosphoribosyltransferase, oligodendrocyte transcription factor 1, pleckstrin homology and RhoGEF domain containing G4B, and ENSSSCG00000031548) associated with ADG on the basis of their physiological roles and positional information. These candidate genes are involved in skeletal muscle cell differentiation, diet-induced obesity, and nervous system development.

Conclusion

This study contributes to the identification of the casual mutation that underlies QTLs associated with ADG and to future pig breeding programs based on marker-assisted selection. Further studies are needed to elucidate the role of the identified candidate genes in the physiological processes involved in ADG regulation.