Genetic Diversity Present Within the Near-Complete mtDNA Genome of 17 Breeds of Indigenous Chinese Pigs

Trajectory of livestock genomics in South Asia: A comprehensive review

Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.

Complete mitochondrial genome of Min pig in nucleus herd

In this study, the complete mitochondrial genome of Min pig (Sus scrofa) in nucleus herd was sequenced in order to develop the mitogenome data for genus Sus. The complete mitogenome sequence is 16,719 bp in length, containing a D-loop region, 13 protein-coding genes, 2 ribosomal RNA, and 22 transfer RNA genes. The new sequenced complete mitogenome of Min pig in nucleus herd will provide useful information for application in conservation genetics and evolution for this Near Threatened pig genomes.

Genetic Diversities and Differentially Selected Regions Between Shandong Indigenous Pig Breeds and Western Pig Breeds

Shandong indigenous pig breeds are an invaluable source of data on genetics in Chinese pigs. However, information on the genetic basis of these breeds remains limited. In this study, we used specific-locus amplified fragment sequencing to conduct whole-genome screening to investigate genetic diversity in Shandong indigenous breeds and Western pig breeds. The results showed that Duroc pigs (DD) had clear genetic relationships with Dapulian pigs (DPL; Fst = 0.4386) and Laiwu pigs (LW; Fst = 0.5134), and DPL and LW were relatively close genetically (Fst = 0.2334). In general, Shandong indigenous breeds showed greater genetic variety than the Western breeds. Both neighbor-joining trees and principal components analyses were able to differentiate the breeds, but population structure analyses indicated that the Western breeds genetically influenced the Shandong indigenous breeds to some extent. A total of 162 differentially selected regions (DSRs) with 841 genes and 157 DSRs with 707 genes were identified in DPL and LW, respectively. Gene annotation of the selected regions identified a series of genes regulating immunity and fat deposition. Our data confirm the rationality and accuracy of the current classification of pig breeds in Shandong province. Our results point to candidate genes in Shandong indigenous pig breeds and further promote the importance of follow-up research on functional verification.

Multiple Domestication Centers Revealed by the Geographical Distribution of Chinese Native Pigs

Previous studies have shown that Southeast Asian pigs were independently domesticated from local wild boars. However, the domestication of Chinese native pigs remains a subject of debate. In the present study, phylogenetic analysis of Chinese native pigs was performed by screening for haplotypes inferred from a phylogenetic tree of pig mitochondrial DNA (mtDNA) sequences based on sequence-specific mutations. A total of 2466 domestic pigs formed 124 haplotypes and were assigned to four clades. Clade A comprised pigs distributed mainly in the Qinghai-Tibet Plateau and its surrounding areas; these pigs clustered into three groups. The pigs of clade B were mainly from the Mekong River Basin in Yunnan Province and had been exposed to genetic infiltration from European populations. Clade C comprised pigs mainly from the middle and lower reaches of the Yangtze River. The pigs of clade D were distributed mainly at the intersection of Yunnan, Sichuan, and Gansu provinces east of the Hengduan Mountains (YSGH). Compared with wild boar, at least three domestication centers and one expansion center of pigs in China were detected. Among the four centers detected, two were for Tibetan pigs and were in the Qinghai-Tibet Plateau and at the YSGH intersection, and the other two were in the Mekong River Basin in Yunnan Province and the middle and downstream regions of the Yangtze River.

Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array

Simple Summary

The pig is one of the most important livestock animals, providing the majority of protein for humans. The population genetics analysis of pigs not only helps humans understand the domestication of the pig but also helps breeders in the genetic improvement of pigs. In this study, the population genetics of 11 pig breeds of South China were analyzed with the help of single nucleotide polymorphism (SNP) chips. The results showed that the genetic diversity of South China indigenous pigs is declining rapidly, and gene introgression from commercial pigs to indigenous pigs was detected. Selection signature analysis showed differences among South China indigenous pig breeds, commercial pig breeds, and wild pig breeds were present for meat quality and growth. Our study deepened understanding of the conservation status and selection mechanisms of Chinese indigenous pigs.

Abstract

To investigate the genetic diversity, population structure, extent of linkage disequilibrium (LD), effective population size (Ne), and selection signatures in indigenous pigs from Guangdong and Guangxi in China, 226 pigs belonging to ten diverse populations were genotyped using single nucleotide polymorphism (SNP) chips. The genetic divergence between Chinese and Western pigs was determined based on the SNP chip data. Low genetic diversity of Dahuabai (DHB), Luchuan (LC), Lantang (LT), and Meihua (MH) pigs, and introgression of Western pigs into Longlin (LL), MH, and Yuedonghei (YDH) pigs were detected. Analysis of the extent of LD showed that indigenous pigs had low LD when pairwise SNP distance was short and high LD when pairwise SNP distance was long. Effective population size analysis showed a rapid decrease for Chinese indigenous pigs, and some pig populations had a relatively small Ne. This result indicated the loss of genetic diversity in indigenous pigs, and introgression from Western commercial pigs. Selection signatures detected in this study overlapped with meat quality traits, such as drip loss, intramuscular fat content, meat color b*, and average backfat thickness. Our study deepened understanding of the conservation status and domestication of Chinese indigenous pigs.

Population structure and genetic diversity of four Henan pig populations

To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping-by-sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor-joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome-wide association studies.

Genetic diversity and phylogeographic structure of Bactrian camels shown by mitochondrial sequence variations

The Bactrian camel includes various domestic (Camelus bactrianus) and wild (Camelus ferus) breeds that are important for transportation and for their nutritional value. However, there is a lack of extensive information on their genetic diversity and phylogeographic structure. Here, we studied these parameters by examining an 809‐bp mtDNA fragment from 113 individuals, representing 11 domestic breeds, one wild breed and two hybrid individuals. We found 15 different haplotypes, and the phylogenetic analysis suggests that domestic and wild Bactrian camels have two distinct lineages. The analysis of molecular variance placed most of the genetic variance (90.14%, P < 0.01) between wild and domestic camel lineages, suggesting that domestic and wild Bactrian camel do not have the same maternal origin. The analysis of domestic Bactrian camels from different geographical locations found there was no significant genetic divergence in China, Russia and Mongolia. This suggests a strong gene flow due to wide movement of domestic Bactrian camels.

The complete mitochondrial genome of Juema pig Sus scrofa (Suina: Suidae) from southern Gansu

Juema pig is a kind of rare and special pig which is well adapted to high altitude, cold climate and harsh natural environment. The complete mitochondrial genome of Juema pig Sus scrofa is a circular molecule of 16 532 bp in length, containing 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and a control region. The A + T content of the overall base composition of H-strand is 60.7% (T: 26.2%; C: 26.0%; A: 34.5%; G: 13.3%). ND4L gene begins with GTG as start codon, ND2, ND3, and ND5 genes begin with ATA as a start codon, and other nine protein-coding genes start with ATG. Cyt b gene is terminated with AGA as stop codon, ND1 and ND2 genes are terminated with TAG as stop codon, COII, COIII, ND3, and ND4 end with T, while ATP6, ATP8, COI, ND4L, ND5, and ND6 end with TAA. In addition, the phylogenetic relationships from neighbor-joining analyses based on the 13 concatenated PCGs indicated (Tylopoda (Suina (Ruminantia (Hippopotamidae, Cetacea)))).

Detecting mitochondrial signatures of selection in wild Tibetan pigs and domesticated pigs

Selection in genomic regions is prevalent in mammals; however, the effects of selection on the mitogenome are not clearly understood. We determined the complete mitochondrial DNA (mtDNA) sequences from six wild Tibetan pigs from the Tibetan plateau and four domestic pig breeds from the lowland of neighboring southwest China. Nucleotide diversity analysis using the sliding window method showed that the nucleotide diversity of wild Tibetan pigs in most regions of the mitogenome was higher than that of domestic pigs. The 12 s ribosomal RNA showed relatively lower nucleotide diversity in Tibetan pigs, suggesting purifying selection of these genes during high-altitude adaptation. More non-synonymous nucleotide substitutions in the ATP6 were found in wild Tibetan pigs, indicating adaptive selection in Tibetan pigs. The results suggested distinct impacts of natural selection and artificial selection upon the mitogenome, especially the mitochondrial signatures of adaptive evolution in wild Tibetan pigs under natural selection.

The phylogenetic status of typical Chinese native pigs: analyzed by Asian and European pig mitochondrial genome sequences

China is one of the most diverse countries, which have developed 88 indigenous pig breeds. Several studies showed that pigs were independently domesticated in multiple regions of the world. The purpose of this study was to investigate the origin and evolution of Chinese pigs using complete mitochondrial genomic sequences (mtDNA) from Asian and European domestic pigs and wild boars. Thirty primer pairs were designed to determine the mtDNA sequences of Xiang pig, Large White, Lantang, Jinhua and Pietrain. The phylogenetic status of Chinese native pigs was investigated by comparing the mtDNA sequences of complete coding regions and D-loop regions respectively amongst Asian breeds, European breeds and wild boars. The analyzed results by two cluster methods contributed to the same conclusion that all pigs were classified into two major groups, European clade and Asian clade. It revealed that Chinese pigs were only recently diverged from each other and distinctly different from European pigs. Berkshire was clustered with Asian pigs and Chinese pigs were involved in the development of Berkshire breeding. The Malaysian wild boar had distant genetic relationship with European and Asian pigs. Jinhua and Lanyu pigs had more nucleotide diversity with Chinese pigs although they all belonged to the Asian major clade. Chinese domestic pigs were clustered with wild boars in Yangtze River region and South China.

Identification of mtDNA lineages of Sus scrofa by multiplex single base extension for the authentication of processed food products

A genetic method to identify the breed of origin could serve as a useful tool for inspecting the authenticity of the increasing number of monobreed foodstuffs, such as those derived from small local European pig breeds. Mitochondrial DNA (mtDNA) is practically the only reliable genomic target for PCR in processed products, and its haploid nature and strict maternal inheritance greatly facilitate genetic analysis. As a result of strategies that sought to improve the production traits of European pigs, most industrial breeds presently show a high frequency of Asian alleles, while the absence or low frequency of such Asian alleles has been observed in small rustic breeds from which highly prized dry-cured and other traditional products are derived. Therefore, the detection of Asian ancestry would indicate nonconformity in Protected Denomination of Origin products. This study presents a single base extension assay based on 15 diagnostic mtDNA single nucleotide polymorphisms to discriminate between Asian and European Sus scrofa lineages. The test was robust, sensitive and accurate in a wide range of processed foodstuffs and allowed accurate detection of pig genetic material and identification of maternal ancestry. A market survey suggested that nonconformity of products derived from Portuguese breeds is an unusual event at present, but regular surveys both in the local populations and in commercial products would be advisible. Taking into consideration the limitations presented by other methodologies, this mtDNA-based test probably attains the highest resolution for the direct genetic test for population of origin in Sus scrofa food products.

Genetic variations and sequences analysis of MTATP6 and MTATP8 genes among different Chinese pig breeds

To investigate the genetic variations of mtATP6 and mtATP8 genes among different Chinese pig breeds, two fragments of 425 and 743 bp containing the whole coding region of mtATP8 and mtATP6 genes were amplified with 805 individuals from 23 Chinese local pig breeds, three types of Chinese wild boars and three European pig breeds. Sequence comparison identified a total number of 17 substitutions including six variable sites in mtATP8 and eleven substitutions in mtATP6 gene. The restriction enzyme Fok I revealed four polymorphic sites (nt8086, 8176, 8514 and 7784), and four RFLP haplotype patterns (A, B, C and D) were identified in mtATP6 and mtATP8 genes among all tested samples. Our data showed AC combined haplotype originated from Asia and BD was regarded as European origin. The average frequency of Asian mtDNA haplotypes was 38.3% across the investigated European breeds but varied within each breeds (13.3∼76.7%). Phylogenetic analyses were performed also considering some published sequences in the databases; the sequences were divided into three distinct groups, denoted A, E1, and E2. The Asian AC haplotype existed among the European domestic pigs was fully consistent with the results of previous molecular studies and well-documented history. This study will help us to better understand the genetic variations of mitochondrial genes among different Chinese pig breeds.

The robust phylogeny of Korean wild boar (Sus scrofa coreanus) using partial D-loop sequence of mtDNA

In order to elucidate the precise phylogenetic relationships of Korean wild boar (Sus scrofa coreanus), a partial mtDNA D-loop region (1,274 bp, NC_000845 nucleotide positions 16576-1236) was sequenced among 56 Korean wild boars. In total, 25 haplotypes were identified and classified into four distinct subgroups (K1 to K4) based on Bayesian phylogenetic analysis using Markov chain Monte Carlo methods. An extended analysis, adding 139 wild boars sampled worldwide, confirmed that Korean wild boars clearly belong to the Asian wild boar cluster. Unexpectedly, the Myanmarese/Thai wild boar population was detected on the same branch as Korean wild boar subgroups K3 and K4. A parsimonious median-joining network analysis including all Asian wild boar haplotypes again revealed four maternal lineages of Korean wild boars, which corresponded to the four Korean wild boar subgroups identified previously. In an additional analysis, we supplemented the Asian wild boar network with 34 Korean and Chinese domestic pig haplotypes. We found only one haplotype, C31, that was shared by Chinese wild, Chinese domestic and Korean domestic pigs. In contrast to our expectation that Korean wild boars contributed to the gene pool of Korean native pigs, these data clearly suggest that Korean native pigs would be introduced from China after domestication from Chinese wild boars.

Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia

A fine-grained mitochondrial DNA phylogenomic analysis was conducted in domestic pigs and wild boars, revealing that pig domestication in East Asia occurred in the Mekong and the middle and downstream regions of the Yangtze river.

Background

Previously reported evidence indicates that pigs were independently domesticated in multiple places throughout the world. However, a detailed picture of the origin and dispersal of domestic pigs in East Asia has not yet been reported.

Results

Population phylogenomic analysis was conducted in domestic pigs and wild boars by screening the haplogroup-specific mutation motifs inferred from a phylogenetic tree of pig complete mitochondrial DNA (mtDNA) sequences. All domestic pigs are clustered into single clade D (which contains subclades D1, D2, D3, and D4), with wild boars from East Asia being interspersed. Three haplogroups within D1 are dominant in the Mekong region (D1a2 and D1b) and the middle and downstream regions of the Yangtze River (D1a1a), and may represent independent founders of domestic pigs. None of the domestic pig samples from North East Asia, the Yellow River region, and the upstream region of the Yangtze River share the same haplogroup status with the local wild boars. The limited regional distributions of haplogroups D1 (including its subhaplogroups), D2, D3, and D4 in domestic pigs suggest at least two different in situ domestication events.

Conclusion

The use of fine-grained mtDNA phylogenomic analysis of wild boars and domestic pigs is a powerful tool with which to discern the origin of domestic pigs. Our findings show that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River.

Ancient vs. recent processes as factors shaping the genetic variation of the European wild boar: are the effects of the last glaciation still detectable?

The European wild boar is an important game species, subjected to local extinctions and translocations in the past, and currently enormously and worryingly expanding in some areas where management is urgently required. Understanding the relative roles of ancient and recent events in shaping the genetic structure of this species is therefore not only an interesting scientific issue, but it represents also the basis for addressing future management strategies. In addition, several pig breeds descend from the European wild boar, but the geographical location of the domestication area(s) and the possible introgression of pig genomes into wild populations are still open questions. Here, we analysed the genetic variation in different wild boar populations in Europe. Ten polymorphic microsatellites were typed in 252 wild boars and the mtDNA control region was sequenced in a subset of 145 individuals. Some samples from different pig breeds were also analysed. Our results, which were obtained considering also 612 published mtDNA sequences, suggest that (i) most populations are similarly differentiated, but the major discontinuity is found along the Alps; (ii) except for the Italian populations, European wild boars show the signature of a postglacial demographic expansion; (iii) Italian populations seem to preserve a high proportion of preglaciation diversity; (iv) the demographic decline which occurred in some areas in the last few centuries did not produce a noticeable reduction of genetic variation; (v) signs of human-mediated gene flow among populations are weak, although in some regions the effects of translocations are detectable and a low degree of pig introgression can be identified; (vi) the hypothesis of an independent domestication centre in Italy is not supported by our data, which in turn confirm that Central European wild boar might have represented an important source for domestic breeds. We can therefore conclude that recent human activities had a limited effect on the wild boar genetic structure. It follows that areas with high variation and differentiation represent natural reservoirs of genetic diversity to be protected avoiding translocations. In this context controlling some populations by hunting is not expected to affect significantly genetic variation in this species.

Interpopulation and intrapopulation maternal lineage genetics of the Lanyu pig (Sus scrofa) by analysis of mitochondrial cytochrome b and control region sequences

The Lanyu pig is an indigenous breed from the Lanyu Islet, which is southeast of Taiwan. Two herds of Lanyu pigs were introduced from the Lanyu Islet into Taiwan in 1975 and 1980. The current population of conserved Lanyu pigs consists of only 44 animals with unknown genetic lineage. The Lanyu pig possesses a distinct maternal genetic lineage remote from Asian and European pigs. The present study aimed to understand the phylogenetic relationship among conserved Lanyu, Asian, and European type pigs based on the cytochrome b coding gene, to ascertain the maternal lineage and genetic diversity within the conserved Lanyu pigs, and to address whether genetic introgression from exotic or Formosan wild pigs had occurred in the conserved Lanyu pigs. Entire mitochondrial genomes of both types of Lanyu pig comprised 2 ribosomal RNA, 22 transfer RNA, and 13 protein-coding genes. Only 2 haplotypes of the mitochondrial DNA (mtDNA) control region and cytochrome b were identified in the conserved Lanyu pig herds. When maximum likelihood trees were constructed, the Type I Lanyu mitochondrial genes formed a unique clade with a large pairwise distance of both cytochrome b and the control region from Asian and European type breeds, Formosan wild pigs, and exotic breeds. Significant loss of genetic diversity of mtDNA within the conserved Lanyu pigs was demonstrated by low haplotype and nucleotide diversities, supported by Fu and Li's D* neutrality test (1.44055; P < 0.05). The mtDNA control region sequences of extant pigs in the Lanyu Islet, however, showed high haplotype and nucleotide diversity, and clustered with exotic pigs. These results indicate no maternal lineage mtD-NA gene introgression from Formosan wild pigs and introduced exotic pigs to conserved Type I Lanyu pigs, and a severe loss of heterozygosity of mtDNA in conserved Lanyu pigs. The remaining extant pigs on the Lanyu Islet have been introgressed with exotic breeds. Strategies for future conservation of native Lanyu pigs are now even more urgent and important.

The pygmy hog is a unique genus: 19th century taxonomists got it right first time round

The pygmy hog, Sus salvanius, the smallest and rarest extant suid was first described as the only member of the genus Porcula. It is currently regarded as member of the genus Sus and a sister taxon of the domestic pig/Eurasian wild boar (Sus scrofa). Phylogenetic analyses of 2316 bp from three mtDNA loci (control-region, cytochrome b, 16S) by Bayesian inference and statistical testing of alternative phylogenetic hypotheses all support the original classification of the pygmy hog as a unique genus. Thus, we propose that the species name Porcula salvania should be resurrected. The reclassification will heighten awareness of the need for the future protection and survival of this unique species.

Mitochondrial DNA Polymorphism and Determination of Effects on Reproductive Trait in Pigs

The purposes of this study were to investigate single strand conformation polymorphisms (SSCP) in the D-loop region of pig mitochondrial DNA (mtDNA) and to determinate their association with the reproductive traits of meishan pigs. A total of four types of band patterns, designed SSCP band pattern A, B, C and D, were identified. A type of SSCP band pattern was present in all European-American breeds, but not in East Asian breeds. This result showed the diversified sequence in the D-loop region between European-American and East Asian populations. Two types of band patterns, B and C, were found in Meishan pigs. The average body weight at day 21 of piglets from B type dams was significantly heavier than the body weight of C type (p < 0.05). We also tested whether the SSCP patterns would be suitable for paternity testing in a family group and found that bands of all the offspring were derived from their maternal parent. Therefore, we conclude that SSCP may be a marker for identification of maternal ancestors.

Relatively well preserved DNA is present in the crystal aggregates of fossil bones

DNA from fossil human bones could provide invaluable information about population migrations, genetic relations between different groups and the spread of diseases. The use of ancient DNA from bones to study the genetics of past populations is, however, very often compromised by the altered and degraded state of preservation of the extracted material. The universally observed postmortem degradation, together with the real possibility of contamination with modern human DNA, makes the acquisition of reliable data, from humans in particular, very difficult. We demonstrate that relatively well preserved DNA is occluded within clusters of intergrown bone crystals that are resistant to disaggregation by the strong oxidant NaOCl. We obtained reproducible authentic sequences from both modern and ancient animal bones, including humans, from DNA extracts of crystal aggregates. The treatment with NaOCl also minimizes the possibility of modern DNA contamination. We thus demonstrate the presence of a privileged niche within fossil bone, which contains DNA in a better state of preservation than the DNA present in the total bone. This counterintuitive approach to extracting relatively well preserved DNA from bones significantly improves the chances of obtaining authentic ancient DNA sequences, especially from human bones.

The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.

Phylogenetic relationships of Australian and New Zealand feral pigs assessed by mitochondrial control region sequence and nuclear GPIP genotype

Pigs were introduced into Australia and New Zealand in the 18th and 19th centuries, with some establishing feral populations. With few records of pig introductions into these two countries, molecular phylogenetic analysis was used to assess their origins. Mitochondrial (mt) control region sequence and nuclear glucosephosphate isomerase pseudogene (GPIP) restriction fragments were used, as distinct European and Asian domestic pig and Wild Boar control region clades and GPIP genotypes can be recognised. Feral pig control region sequences clustered with either European or Asian domestic pig sequences and both Asian and European GPIP alleles were segregating. It was not possible to distinguish direct importation of Asian domestic animals into Australia and New Zealand from indirect introgression of Asian domestic sequences via Europe. However, the clustering of three feral control region sequences of pigs from northern Australia with Asian Wild Boar implies unrecorded introduction of Wild Boar or crossbred animals into Australia. However, two of these feral pigs had European GPIP alleles. In combination, analyses of control region and GPIP markers suggest that both European and Asian pigs have contributed in similar frequencies to the origins of Australian feral pigs.