Asia-wide phylogeography of wild boar (Sus scrofa) based on mitochondrial DNA and Y-chromosome: Revising the migration routes of wild boar in Asia

Phylogenetic Relations and High-Altitude Adaptation in Wild Boar (Sus scrofa), Identified Using Genome-Wide Data

The Qinghai-Tibet Plateau (QTP) wild boar is an excellent model for investigating high-altitude adaptation. In this study, we analyzed genome-wide data from 93 wild boars compiled from various studies worldwide, including the QTP, southern and northern regions of China, Europe, Northeast Asia, and Southeast Asia, to explore their phylogenetic patterns and high-altitude adaptation based on genome-wide selection signal analysis and run of homozygosity (ROH) estimation. The findings demonstrate the alignment between the phylogenetic associations among wild boars and their geographical location. An ADMIXTURE analysis indicated a relatively close genetic relationship between QTP and southern Chinese wild boars. Analyses of the fixation index and cross-population extended haplotype homozygosity between populations revealed 295 candidate genes (CDGs) associated with high-altitude adaptation, such as TSC2, TELO2, SLC5A1, and SLC5A4. These CDGs were significantly overrepresented in pathways such as the mammalian target of rapamycin signaling and Fanconi anemia pathways. In addition, 39 ROH islands and numerous selective CDGs (e.g., SLC5A1, SLC5A4, and VCP), which are implicated in glucose metabolism and mitochondrial function, were discovered in QTP wild boars. This study not only assessed the phylogenetic history of QTP wild boars but also advanced our comprehension of the genetic mechanisms underlying the adaptation of wild boars to high altitudes.

Blastocystis occurrence and subtype diversity in European wild boar (Sus scrofa) from the Iberian Peninsula

The ongoing increase in wild boar populations across Europe has fostered human-wildlife conflicts, including the transmission of emerging pathogens with zoonotic importance. Blastocystis is a ubiquitous, faecal-oral transmitted protist that can cause gastrointestinal illnesses and is observed in humans and animals worldwide. The role of wildlife in the epidemiology of Blastocystis is insufficiently understood. Thus, we investigated the occurrence and subtype diversity of Blastocystis in free-ranging wild boars from the Iberian Peninsula using conventional PCR and next-generation amplicon sequencing of a fragment of the ssu RNA gene. A total of 459 wild boar faecal samples were collected across Spain (n = 360) and Portugal (n = 99) between 2014 and 2021. Blastocystis was present in 15.3% (70/459; 95% CI 12.1-18.9) of the wild boars analysed, and its occurrence was significantly higher in Portugal (34.3%, 34/99; 95% CI 25.1-44.6) than in Spain (10.0%, 36/360; 95% CI 7.1-13.6). Seven Blastocystis subtypes (ST5, ST10b, ST13-ST15, ST24b, and ST43) were detected among the surveyed wild boar populations, with greater variability detected in Portuguese samples. ST5 was identified in all the Blastocystis-positive animals, whereas 14.3% of them harboured ST mixed colonisations. Our results demonstrate that Blastocystis ST5 is particularly adapted to infect wild boars. The additional identification of zoonotic STs reinforces the role of wild boars as spreaders of zoonotic infections with public health significance.

A chromosome-level genome of Chenghua pig provides new insights into the domestication and local adaptation of pigs

As a country with abundant genetic resources of pigs, the domestication history of pigs in China and the adaptive evolution of Chinese pig breeds at different latitudes have rarely been elucidated at the genome-wide level. To fill this gap, we first assembled a high-quality chromosome-level genome of the Chenghua pig and used it as a benchmark to analyse the genomes of 272 samples from three genera of three continents. The divergence of the three species belonging to three genera, Phacochoerus africanus, Potamochoerus porcus, and Sus scrofa, was assessed. The introgression of pig breeds redefined that the migration routes were basically from southern China to central and southwestern China, then spread to eastern China, arrived in northern China, and finally reached Europe. The domestication of pigs in China occurred ∼12,000 years ago, earlier than the available Chinese archaeological domestication evidence. In addition, FBN1 and NR6A1 were identified in our study as candidate genes related to extreme skin thickness differences in Eurasian pig breeds and adaptive evolution at different latitudes in Chinese pig breeds, respectively. Our study provides a new resource for the pig genomic pool and refines our understanding of pig genetic diversity, domestication, migration, and adaptive evolution at different latitudes.

Tracing the genetic footprints: India's role as a gateway for pig migration and domestication across continents

This study explored the maternal genetic diversity in the pig genetic resources of India by analyzing a mitochondrial D-loop fragment and comparing it with the corresponding sequences of previously published studies involving domestic pigs and wild boars. Sequencing of 103 samples representing different domestic pig populations revealed existence of 32 maternal haplotypes. The indices of haplotype and nucleotide diversity in Indian domestic pigs were 0.9421 and 0.015, respectively. Median-Joining network revealed that Indian pigs belong to Clade A and show conformity to 6 haplogroups reported worldwide (D1a, D1a1, D1a2, D1e, D1h and D3a). Among these, D1e and D1a2 were shared with Asian wild boars too. Interestingly, haplotype sharing was evident between Indian pigs and samples from other countries representing Africa, Asia, Europe and Oceania. This study substantiates India's contribution as a possible pig domestication center and highlights the importance of the Indian subcontinent in dispersal of the species to other continents. Additionally, genetic evidence suggested the influence of trading routes and historical interactions in shaping pig genetic exchange. Overall, this investigation provides valuable insights into the genetic diversity, historical migration, and domestication of Indian domestic pigs, contributing to the broader understanding of global pig genetic resources and their evolutionary history.

Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys

To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise F_ST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.

Genome-Wide Selection Signal Analysis to Investigate Wide Genomic Heredity Divergence between Eurasian Wild Boar and Domestic Pig

As important livestock species, pigs provide essential meat resources for humans, so understanding the genetic evolution behind their domestic history could help with the genetic improvement of domestic pigs. This study aimed to investigate the evolution of convergence and divergence under selection in European and Asian domestic pigs by using public genome-wide data. A total of 164 and 108 candidate genes (CDGs) were obtained from the Asian group (wild boar vs. domestic pig) and the European group (wild boar vs. domestic pig), respectively, by taking the top 5% of intersected windows of a pairwise fixation index (FST) and a cross population extended haplotype homozygosity test (XPEHH). GO and KEGG annotated results indicated that most CDGs were related to reproduction and immunity in the Asian group. Conversely, rich CDGs were enriched in muscle development and digestion in the European group. Eight CDGs were subjected to parallel selection of Eurasian domestic pigs from local wild boars during domestication. These CDGs were mainly involved in olfactory transduction, metabolic pathways, and progesterone-mediated oocyte maturation. Moreover, 36 and 18 haplotypes of INPP5B and TRAK2 were identified in this study, respectively. In brief, this study did not only improve the understanding of the genetic evolution of domestication in pigs, but also provides valuable CDGs for future breeding and genetic improvement of pigs.

Phylogeny and Genetic Diversity of Philippine Native Pigs (Sus scrofa) as Revealed by Mitochondrial DNA Analysis

Philippine native pigs (PhNP) are small black pigs domesticated in rural communities in the Philippines. They are valued locally for their various sociocultural roles. Recently, considerable literature has accumulated in the field of native pig production and marketing. However, there is limited research on the genetic diversity of PhNP. No previous study has investigated the evolutionary relatedness among native pigs from various islands and provinces in Luzon and the Visayas, Philippines. In addition, a much debated question is whether the PhNP were interbreeding with or even domesticated from endemic wild pigs. This study aims to clarify some of the uncertainties surrounding the identity and classification of PhNP based on mitochondrial DNA (mtDNA) signatures. Native pig samples (n = 157) were collected from 10 provinces in Luzon and the Visayas. Approximately 650 base pairs of the mtDNA D-loop region were sequenced and analyzed together with publicly available sequences. Pairwise-distance analysis showed genetic separation of North and South Luzon (SL) and the clustering of SL with Visayan pigs. Phylogenetic analysis showed that the PhNP clustered within 3 recognized Asian pig domestication centers: D2 (East Asia), D7 (Southeast Asia) and the Cordillera clade (sister to the Lanyu). We identified 19 haplotypes (1-38 samples each), forming 4 haplogroups, i.e., North Luzon, South Luzon and Visayas, Asian mix and the Cordillera cluster. No endemic wild pig mtDNA was detected in the native pig population, but evidence of interspecific hybridization was observed. This study showed that the Philippine native pigs have originated from at least 3 Sus scrofa lineage and that they were not domesticated from the endemic wild pigs of the Philippines.

Genetic Diversity of Wild Boar and Deer

Genetic diversity provides the long-term capacity of species, communities, and the biosphere to persist under change [...].

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.

Genotype Shift of Malaysian Porcine Circovirus 2 (PCV2) from PCV2b to PCV2d within a Decade

This paper aims to update the molecular status of porcine circovirus 2 (PCV2) in Malaysia. Firstly, the molecular detection rate of PCV2 in farm and sampled pig population were reported to be 83.78% (31/37 farms) and 83.54% (66/79 pigs) positive for PCV2, respectively. PCV2 was detected across all age groups, from fetuses, porkers to sows. Co-detection of PCV2 and PCV3 antigens was also reported at a rate of 28.77% (21/73). Secondly, PCV2 antigen was also detected in Malaysian abattoir lung samples: 18 out of 19 (94.74%) samples originating from clinically healthy finishers were tested positive. Further, this is the first study to confirm the circulation of PCV2 in the wild boar population roaming Peninsular Malaysia, where 28 out of 28 (100%) wild boar lung samples were found positive. One decade earlier, only genotype PCV2b was reported in Malaysia. This most recent update revealed that genotypes PCV2a, PCV2b and PCV2d were present, with PCV2d being the predominant circulating genotype. PCV2 cap gene nucleotide sequences in this study were found to be under negative selection pressure, with an estimated substitution rate of 1.102 × 10-3 substitutions/site/year (ssy).

Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19^th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.

Population Source of Third-Generation Oriental Armyworm in Jilin, China, Determined by Entomology Radar, Trajectory Analysis, and Mitochondrial COI Sequences

The armyworm, Mythimna separata (Walker) (Lepidoptera: Noctuidae), is an important polyphagous pest with a strong migratory ability. Recently, third-generation larvae have become an increasingly serious pest threat in Jilin Province of northeast China. To investigate the population source of this species, scanning entomological radar observations and insect mitochondrial cytochrome oxidase I (COI) genes were used in this study. Five main results were found: (1) The peak period in captured second-generation moths was from mid to late July. The temperature and wind speeds were optimum for the moths to have migrated. Strong southwesterly winds occurred during the peak migration period. (2) Radar observations indicated that most of the moths' migration took place at a height of 600 m, often in a dense layer which formed at heights of 350-800 m. (3) Analyses of adult ovarian development and larval haplotypes showed third-generation larvae were progeny of both locally produced progeny and immigrant moths. (4) Based on our back-tracking and haplotype analyses, immigration led to an outbreak originated in the same source area to the southwest. (5) Emigration of second-generation moths was confirmed by both radar observation and mtDNA analysis. Forward trajectories indicated that the moths were capable of immigrating far from their overwintering range. These results are useful for improving the forecasting systems of this insect pest species.

Identification of candidate genes associated with bacterial and viral infections in wild boars hunted in Tuscany (Italy)

Wild boar (Sus scrofa L.) is one of the large mammals most spread worldwide, highly adaptable, and its population rapidly increased in many areas in Europe, including Italy, where Tuscany is considered particularly suitable for wild boar. Wild boars are potential hosts for different etiological agents, such as Brucella spp., Leptospira spp. and Pseudorabies virus and they can contribute to maintain and/or to disseminate some bacterial or viral pathogens to humans and domestic animals, above all-in free-range farms. In order to identify hypothetical genomic regions associated with these infection diseases, 96 samples of wild boars hunted in Tuscany during the 2018-2019 and 2019-2020 hunting seasons were considered. Diagnosis was achieved by serological tests and 42 Pseudorabies, 31 Leptospira and 15 Brucella positive animals were identified. All animals were genotyped with Geneseek Genomic Profiler Porcine HD (70 k) and a genome-wide scan was then performed. Significant markers were highlighted for Pseudorabies (two SNPs), Brucella (seven SNPs), and Leptospira (four SNPs) and they were located within, or nearby, 29 annotated genes on chromosome 6, 9, 12, 13, 14 and 18. Eight genes are implicated in viral (SEC14L1, JMJD6, SRSF2, TMPRSS2, MX1, MX2) or bacterial (COL8A1, SPIRE1) infections, seven genes (MFSD11, METTL23, CTTNBP2, BACE2, IMPA2, MPPE1 and GNAL) are involved in mental disorders and one gene (MGAT5B) is related to the Golgi complex. Results presented here provide interesting starting points for future research, validation studies and fine mapping of candidate genes involved in bacterial and viral infections in wild boar.

Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels

Camels represent an important genetic resource of the desert ecosystems of India, with the dromedary and Bactrian camels inhabiting the hot and cold deserts, respectively. This study is the first attempt to investigate mitochondrial DNA based genetic diversity in the Indian camel populations and explores their relationship in the context of global genetic diversity of all the three large camel species (Camelus ferus, Camelus bactrianus and Camelus dromedaries). A mitochondrial DNA fragment encompassing part of cytochrome b gene, tRNA^Thr, tRNA^Pro and the beginning of the control region was amplified and analyzed in 72 dromedary and 8 Bactrian camels of India. Sequence analysis revealed that the haplotype and nucleotide diversity (Hd: 0.937 and π: 0.00431) in the Indian dromedaries was higher than the indices reported so far for the dromedary or Bactrian camels across the globe. The corresponding values in the Indian Bactrian camels were 1.000 and 0.00393, respectively. Signals of population expansion were evident in the dromedaries of India on the basis of mismatch analysis and Fu's Fs values. The analysis of molecular variance attributed most of the genetic variance (92.15%) between the dromedary, wild Bactrian and domestic Bactrian camels indicating separate maternal origins. The existence of three mitochondrial lineages in the old world camels (C. bactrianus: Lineage A; C. ferus: Lineage B and C. dromedarius: Lineage C) was also substantiated by the topology of the Median-Joining network.

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.

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.

Detection of Jingmenviruses in Japan with Evidence of Vertical Transmission in Ticks

Jingmen tick virus (JMTV) and the related jingmenvirus-termed Alongshan virus are recognized as globally emerging human pathogenic tick-borne viruses. These viruses have been detected in various mammals and invertebrates, although their natural transmission cycles remain unknown. JMTV and a novel jingmenvirus, tentatively named Takachi virus (TAKV), have now been identified during a surveillance of tick-borne viruses in Japan. JMTV was shown to be distributed across extensive areas of Japan and has been detected repeatedly at the same collection sites over several years, suggesting viral circulation in natural transmission cycles in these areas. Interestingly, these jingmenviruses may exist in a host tick species-specific manner. Vertical transmission of the virus in host ticks in nature was also indicated by the presence of JMTV in unfed host-questing Amblyomma testudinarium larvae. Further epidemiological surveillance and etiological studies are necessary to assess the status and risk of jingmenvirus infection in Japan.

Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe

The wild boar Sus scrofa is one of the widely spread ungulate species in Europe, yet the origin and genetic structure of the population inhabiting Central and Eastern Europe are not well recognized. We analysed 101 newly obtained sequences of complete mtDNA genomes and 548 D-loop sequences of the species and combined them with previously published data. We identified five phylogenetic clades in Europe with clear phylogeographic pattern. Two of them occurred mainly in western and central part of the continent, while the range of the third clade covered North-Eastern, Central and South-Eastern Europe. The two other clades had rather restricted distribution. In Central Europe, we identified a contact zone of three mtDNA clades. Population genetic structure reflected clear phylogeographic pattern of wild boar in this part of Europe. The contribution of lineages originating from the southern (Dinaric-Balkan) and eastern (northern cost of the Black Sea) areas to the observed phylogeographic pattern of the species in Central and Eastern Europe was larger than those from the regions located in southern France, Iberian, and Italian Peninsulas. The present work was the first mitogenomic analysis conducted in Central and Eastern Europe to study genetic diversity and structure of wild boar population.

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.