Diversity of wild and domestic pig populations estimated by a set of serum allotypes

Variation of serum protein allotypes serving as genetic markers of the blood has been analyzed in 29 populations of the domestic pig and subspecies of the wild boar. The population biodiversity and genetic structure have been estimated by two methods: by the frequencies of allotype combinations and with the use of a map constructed in the space of two principal components. The results obtained are the basis for determining the characteristics of the microevolution of wild boars and formation of the breeds of domestic pigs.     

Maintaining genetic integrity of coexisting wild and domestic populations: Genetic differentiation between wild and domestic Rangifer with long traditions of intentional interbreeding

This study investigates the genetic effect of an indigenous tradition of deliberate and controlled interbreeding between wild and domestic Rangifer . The results are interpreted in the context of conservation concerns and debates on the origin of domestic animals. The study is located in Northeastern Zaba?kal'e, Russia at approximately 57 degrees North latitude. Blood and skin samples, collected from wild and domestic Rangifer , are analyzed for their mtDNA and microsatellite signatures. Local husbandry traditions are documented ethnographically. The genetic data are analyzed with special reference to indigenous understandings of the distinctions between local domestic types and wild Rangifer . The genetic results demonstrate a strong differentiation between wild and domestic populations. Notably low levels of mtDNA haplotype sharing between wild and domestic reindeer, suggest mainly male‐mediated gene flow between the two gene pools. The nuclear microsatellite results also point to distinct differences between regional domestic clusters. Our results indicate that the Evenki herders have an effective breeding technique which, while mixing pedigrees in the short term, guards against wholesale introgression between wild and domestic populations over the long term. They support a model of domestication where wild males and domestic females are selectively interbred, without hybridizing the two populations. Our conclusions inform a debate on the origins of domestication by documenting a situation where both wild and domestic types are in constant interaction. The study further informs a debate in conservation biology by demonstrating that certain types of controlled introgression between wild and domestic types need not reduce genetic diversity.     

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.     

Are wild boars roaming Ireland once more?

Wild boars (Sus scrofa) have been increasingly sighted in the wild in Ireland during the last few years, likely due to illegal releases and/or escapees. The species has since been designated an invasive species in Ireland, which is seen as controversial by some because of uncertainties about the historic status of the species in Ireland. However, just as pertinent to the argument is the genetic purity of these individuals currently found in Ireland: are these pure wild boars? We carried out a genetic assessment of 15 wild boars shot in Ireland between 2009 and 2012 using 14 microsatellites and mitochondrial DNA (mtDNA). These were compared to European wild boar, domestic pig breeds and a hybrid population of ‘wild boar’ from England. Microsatellite analysis revealed that almost all the Irish individuals belonged to the ‘domestic pig’ genetic cluster, with only three individuals being classified as hybrids. All but two individuals carried Asian mtDNA haplotypes, indicating a domestic pig origin. It is clear from this study that the individuals currently found in Ireland are not pure wild boars and this result has to be factored into any management/eradication plans.     

Evidence of infection by H5N2 highly pathogenic avian influenza viruses in healthy wild waterfowl

The potential existence of a wild bird reservoir for highly pathogenic avian influenza (HPAI) has been recently questioned by the spread and the persisting circulation of H5N1 HPAI viruses, responsible for concurrent outbreaks in migratory and domestic birds over Asia, Europe, and Africa. During a large-scale surveillance programme over Eastern Europe, the Middle East, and Africa, we detected avian influenza viruses of H5N2 subtype with a highly pathogenic (HP) viral genotype in healthy birds of two wild waterfowl species sampled in Nigeria. We monitored the survival and regional movements of one of the infected birds through satellite telemetry, providing a rare evidence of a non-lethal natural infection by an HP viral genotype in wild birds. Phylogenetic analysis of the H5N2 viruses revealed close genetic relationships with H5 viruses of low pathogenicity circulating in Eurasian wild and domestic ducks. In addition, genetic analysis did not reveal known gallinaceous poultry adaptive mutations, suggesting that the emergence of HP strains could have taken place in either wild or domestic ducks or in non-gallinaceous species. The presence of coexisting but genetically distinguishable avian influenza viruses with an HP viral genotype in two cohabiting species of wild waterfowl, with evidence of non-lethal infection at least in one species and without evidence of prior extensive circulation of the virus in domestic poultry, suggest that some strains with a potential high pathogenicity for poultry could be maintained in a community of wild waterfowl.     

TYR基因外显子1的序列变异

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

European domestic horses originated in two holocene refugia

The role of European wild horses in horse domestication is poorly understood. While the fossil record for wild horses in Europe prior to horse domestication is scarce, there have been suggestions that wild populations from various European regions might have contributed to the gene pool of domestic horses. To distinguish between regions where domestic populations are mainly descended from local wild stock and those where horses were largely imported, we investigated patterns of genetic diversity in 24 European horse breeds typed at 12 microsatellite loci. The distribution of high levels of genetic diversity in Europe coincides with the distribution of predominantly open landscapes prior to domestication, as suggested by simulation-based vegetation reconstructions, with breeds from Iberia and the Caspian Sea region having significantly higher genetic diversity than breeds from central Europe and the UK, which were largely forested at the time the first domestic horses appear there. Our results suggest that not only the Eastern steppes, but also the Iberian Peninsula provided refugia for wild horses in the Holocene, and that the genetic contribution of these wild populations to local domestic stock may have been considerable. In contrast, the consistently low levels of diversity in central Europe and the UK suggest that domestic horses in these regions largely derive from horses that were imported from the Eastern refugium, the Iberian refugium, or both.     

Ancient DNA from Nubian and Somali wild ass provides insights into donkey ancestry and domestication

Genetic data from extant donkeys (Equus asinus) have revealed two distinct mitochondrial DNA haplogroups, suggestive of two separate domestication events in northeast Africa about 5000 years ago. Without distinct phylogeographic structure in domestic donkey haplogroups and with little information on the genetic makeup of the ancestral African wild ass, however, it has been difficult to identify wild ancestors and geographical origins for the domestic mitochondrial clades. Our analysis of ancient archaeological and historic museum samples provides the first genetic information on the historic Nubian wild ass (Equus africanus africanus), Somali wild ass (Equus africanus somaliensis) and ancient donkey. The results demonstrate that the Nubian wild ass was an ancestor of the first donkey haplogroup. In contrast, the Somali wild ass has considerable mitochondrial divergence from the Nubian wild ass and domestic donkeys. These findings resolve the long-standing issue of the role of the Nubian wild ass in the domestication of the donkey, but raise new questions regarding the second ancestor for the donkey. Our results illustrate the complexity of animal domestication, and have conservation implications for critically endangered Nubian and Somali wild ass.     

The Genetic Integrity of the Ex Situ Population of the European Wildcat (Felis silvestris silvestris) Is Seriously Threatened by Introgression from Domestic Cats (Felis silvestris catus)

Studies on the genetic diversity and relatedness of zoo populations are crucial for implementing successful breeding programmes. The European wildcat, Felis s. silvestris, is subject to intensive conservation measures, including captive breeding and reintroduction. We here present the first systematic genetic analysis of the captive population of Felis s. silvestris in comparison with a natural wild population. We used microsatellites and mtDNA sequencing to assess genetic diversity, structure and integrity of the ex situ population. Our results show that the ex situ population of the European wildcat is highly structured and that it has a higher genetic diversity than the studied wild population. Some genetic clusters matched the breeding lines of certain zoos or groups of zoos that often exchanged individuals. Two mitochondrial haplotype groups were detected in the in situ populations, one of which was closely related to the most common haplotype found in domestic cats, suggesting past introgression in the wild. Although native haplotypes were also found in the captive population, the majority (68%) of captive individuals shared a common mtDNA haplotype with the domestic cat (Felis s. catus). Only six captive individuals (7.7%) were assigned as wildcats in the STRUCTURE analysis (at K = 2), two of which had domestic cat mtDNA haplotypes and only two captive individuals were assigned as purebred wildcats by NewHybrids. These results suggest that the high genetic diversity of the captive population has been caused by admixture with domestic cats. Therefore, the captive population cannot be recommended for further breeding and reintroduction.     

Genome‐wide variation within and between wild and domestic yak

The yak is one of the few animals that can thrive in the harsh environment of the Qinghai‐Tibetan Plateau and adjacent Alpine regions. Yak provides essential resources allowing Tibetans to live at high altitudes. However, genetic variation within and between wild and domestic yak remain unknown. Here, we present a genome‐wide study of the genetic variation within and between wild and domestic yak. Using next‐generation sequencing technology, we resequenced three wild and three domestic yak with a mean of fivefold coverage using our published domestic yak genome as a reference. We identified a total of 8.38 million SNPs (7.14 million novel), 383 241 InDels and 126 352 structural variants between the six yak. We observed higher linkage disequilibrium in domestic yak than in wild yak and a modest but distinct genetic divergence between these two groups. We further identified more than a thousand of potential selected regions (PSRs) for the three domestic yak by scanning the whole genome. These genomic resources can be further used to study genetic diversity and select superior breeds of yak and other bovid species.     

High domestic pig contribution to the local gene pool of free-living European wild boar: a case study in Poland

Rates of hybridization between wild and domesticated animals appear to be increasing worldwide. Recent results suggest that genetic introgression from domestic swine into European wild boar is much more common in local populations than expected, based on pan-European studies. Thus, we screened the genetic purity of 265 free-living wild boars from two hunting areas in Poland by genotyping the melanocortin receptor 1 gene (MC1R) for polymorphism. Unexpectedly, high numbers of individuals with domestic genes (24%) were identified. This suggests that mixed ancestry may be common in Polish wild boar. Among admixed individuals, backcrosses with domestic pig and/or introgressed wild boars were detected (2%). Multiple commercial domestic pig breeds are possibly involved in the introgression observed in the study populations. In addition, the absence of significant differences in the frequency of wild-type allele among two hunting areas suggests high dispersal of individuals and gene flow among populations. We conclude that further study is needed to better understand the mechanisms and sources of introgression in wild boars in Poland.     

Fowl cholera outbreak in domestic poultry and epidemiological properties of Pasteurella multocida isolate

Symptoms of fowl cholera including orofacial edema, swollen and edematous wattles and combs, and severe respiratory disorders were detected in domestic poultry in two broiler breeder farms: one located in Gyeong-gi Province (October, 2000) and the other in Chung-cheong-nam Province (March, 2001). Gram-negative, bipolar staining bacillus was easily found in a direct smear. The biochemical properties of isolates were examined using a standard diagnosis method, proving that they were 99.7% similar to the Pasteurella multocida (P. multocida: PM), a pathogenic and causative agent of fowl cholera (FC). As a result, an FC outbreak in domestic fowls was confirmed for the first time in Korea since 1942. Because FC was detected in broiler breeder farms for the first time in 59 years at the same time as an FC outbreak was confirmed in wild birds (October, 2000), our concern was focused on whether the PM strains that originated in wild birds were transmitted into poultry farms. The possibility was tracked down by comparing phenotypic and genetic properties between the two types of PM strains. PM strains of chicken origin showed prominent differences from the PM strains of wild bird origin in both phenotypic and genetic properties. An examination of the origin of the wild bird bacteria was conducted, but no evidence has been identified that PM strains from the wild bird were introduced into domestic poultry farms.     

Temporal and structural genetic variation in reindeer (Rangifer tarandus) associated with the pastoral transition in Northwestern Siberia

Just as the domestication of livestock is often cited as a key element in the Neolithic transition to settled, the emergence of large‐scaled reindeer husbandry was a fundamental social transformation for the indigenous peoples of Arctic Eurasia. To better understand the history of reindeer domestication, and the genetic processes associated with the pastoral transition in the Eurasian Arctic, we analyzed archaeological and contemporary reindeer samples from Northwestern Siberia. The material represents Rangifer genealogies spanning from 15,000 years ago to the 18th century, as well as modern samples from the wild Ta?myr population and from domestic herds managed by Nenetses. The wild and the domestic population are the largest populations of their kind in Northern Eurasia, and some Nenetses hold their domestic reindeer beside their wild cousins. Our analyses of 197 modern and 223 ancient mitochondrial DNA sequences revealed two genetic clusters, which are interpreted as representing the gene pools of contemporary domestic and past wild reindeer. Among a total of 137 different mitochondrial haplotypes identified in both the modern and archaeological samples, only 21 were detected in the modern domestic gene pool, while 11 of these were absent from the wild gene pool. The significant temporal genetic shift that we associate with the pastoral transition suggests that the emergence and spread of reindeer pastoralism in Northwestern Siberia originated with the translocation and subsequent selective breeding of a special type of animal from outside the region. The distinct and persistent domestic characteristics of the haplotype structure since the 18th century suggests little genetic exchange since then. The absence of the typical domestic clade in modern nearby wild populations suggests that the contemporary Nenets domestic breed feature an ancestry from outside its present main distribution, possibly from further South.     

野牦牛线粒体基因组序列测定及其系统进化

野牦牛属高寒地区的特有物种,是我国最珍贵的野生动物遗传资源之一,已被列为国家一级重点保护动物。对野牦牛mtDNA进行全序列测定和结构分析,并基于线粒体基因组序列对其系统发生进行了探讨。结果表明:(1)野牦牛线粒体基因组全序列的大小为16 322 bp,整个基因组由37个编码基因和D-loop区组成;22个tRNA基因序列长度为1 524 bp、2个RNA基因序列长度为2 528 bp、13个编码蛋白基因序列长度为11420 bp、D-loop区长度为892 bp。基因组中无间隔序列,基因间排列紧密,基因内无内含子。(2)野牦牛具有较丰富的遗传多样性。(3)分子系统发生关系显示牦牛为牛亚科中的一个独立属,即牦牛属(Poephagus),牦牛属包括家牦牛(Poephagus grunniens)和野牦牛(Poephagus mutus)2个种。野牦牛线粒体基因组全序列的获得和结构解析对研究牦牛的起源、演化和分类,以及野牦牛遗传资源的保护、开发和利用均具有重要的理论和实际意义。     

Molecular analysis of hybridisation between wild and domestic cats (Felis silvestris) in Portugal: implications for conservation

The endangered European wildcat (Felis silvestris silvestris) is represented, today, by fragmented and declining populations whose genetic integrity is considered to be seriously threatened by crossbreeding with widespread free-ranging domestic cats. Extensive and recent hybridisation has been described in Hungary and Scotland, in contrast with rare introgression of domestic alleles in Italy and Germany. In Portugal, the wildcat is now listed as VULNERABLE in the Red Book of Portuguese Vertebrates. Nevertheless, genetic diversity of populations and the eventual interbreeding with domestic cats remain poorly studied. We surveyed genetic variation at 12 autosomal microsatellites for 34 wild and 64 domestic cats collected across Portugal. Wild and domestic cats were significantly differentiated both at allele frequencies and sizes (F _ST=0.11, R _ST = 0.18, P < 0.001). Population structure and admixture analyses performed using Bayesian approaches also showed evidence of two discrete groups clustering wild and domestic populations. Results did not show significant genetic divergence among Northern, Central and Southern wildcats. Six morphologically identified wildcats were significantly assigned to the domestic cluster, revealing some discrepancy between phenotypic and genetic identifications. We detected four hybrids (approximately 14%) using a consensus analysis of different Bayesian model-based software. These hybrids were identified throughout all sampled areas, suggesting that hybridisation is of major concern for the appropriate implementation of wildcat conservation strategies in Portugal.     

Are captive wild boar more introgressed than free-ranging wild boar? Two case studies in Italy

Hybridization between wild boar (Sus scrofa) and domestic pig occurred in the past and still occurs today, having great evolutionary and management implications. In fact, genetic introgression from the domestic form may alter traits like behavior, reproduction rate, and immunology in wild populations, with likely demographic impacts. Thus, it is crucial to understand under what conditions hybridization occurs in S. scrofa. Captive crosses with domestic pigs (released or escaped) have been suggested to constitute the major source of the spread of domestic genes into wild boar populations. However, to date, few studies have assessed the degree of admixture in farmed animals in comparison to the surrounding wild populations. With this purpose, we analyzed microsatellite loci in wild boar sampled in breeding stations and in the local wild population in two Italian regions (Sardinia and Piedmont). Both captive populations had lower allelic richness than the corresponding wild population, but a similar expected heterozygosity. In Piedmont, introgression from the domestic form into the wild population seems to be extremely low, while there are significant signs of admixture in the sampled breeding stations. In Sardinia, instead, the captive sample did not differ significantly from the wild population, which showed moderate signs of introgression. We conclude that hybridization in nature seems to play the key role in Sardinia, while intentional hybridization in captivity is the major source of introgression in Piedmont. Our findings emphasize the need for a routine genetic monitoring of wild boar captive populations, coupled with reference data on the neighboring wild populations.     

中国野桑蚕遗传多样性的AFLP分析

采用AFLP技术对我国具有代表性的7个省市的10个野桑蚕(Bombyx mandarina)种群和2个家蚕（Bombyx mori)品种的遗传多样性进行了研究。结果表明：杭州、陕西和重庆3个地区的野桑蚕种群间及种群内个体间的遗传距离都比家蚕品种大。野桑蚕存在广泛的变异,7个省市的10个野桑蚕种群之间的遗传距离为0．164－0．444（平均值为0．3826）,平均杂合度为0．7061,表明野桑蚕自然群体的遗传多样性十分丰富。     

Genetic evidence for introgression between domestic pigs and wild boars (Sus scrofa) in Belgium and Luxembourg: a comparative approach with multiple marker systems

Hybridization between wild species and their domestic relatives can be an important conservation and management problem. Genetic purity of the wild species is desirable per se and the phenomenon can have unpredictable evolutionary consequences. Declining European wild boar populations were frequently restocked with farmed wild boars that sometimes had been crossed with domestic pigs. We used simple polymerase chain reaction‐based diagnostic tests to detect the presence of mitochondrial DNA and coat colour alleles of domestic origin in wild boars from Belgium, Luxembourg, and western Germany. Microsatellite genotypes were used to test for genetic admixture between the wild boars and domestic pigs. Although almost one‐third of all Luxembourg wild boars carried Asian mitochondrial DNA haplotypes originating from domestic pigs, microsatellite‐based clustering only identified four putatively admixed individuals in Luxembourg. By contrast, clustering identified wild boar × domestic hybrids in most sampling locations in Belgium. We interpret these results as evidence of releases of hybrid captive‐reared wild boars. Our results emphasize the need (if working with classical markers) to use different systems to obtain an understanding as to whether hybridization between wild and domestic relatives might have affected the genetic make‐up of a local population. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 104–115.     

A genetic method to distinguish crossbred Inobuta from Japanese wild boars

To distinguish pig-wild boar crossbred Inobuta from Japanese wild boar populations, a genetic method by using mitochondrial DNA (mtDNA) haplotypes and the nuclear glucosephosphate isomerase-processed pseudogene (GPIP) was developed. Sixteen mtDNA haplotypes from 152 wild boars from Kyushu, Shikoku and Honshu islands of Japan were distinct from those from Asian and European domestic pigs. Five alleles of GPIP were classified into two groups: 1). alleles GPIP*1, GPIP*3 and GPIP*3a from Japanese wild boars, Asian wild boars and domestic pigs; 2). alleles GPIP*4 and GPIP*4a from European wild boars and domestic pigs. An extensive genetic survey was done to distinguish the crossbred Inobuta from 60 wild boars hunted on Tsushima Island, Goto Islands, and Nagasaki and Ooita Prefectures. The mtDNA haplotypes from the 60 samples showed Japanese wild boars, but four wild boar samples from Nagasaki Prefecture had the European GPIP allele, GPIP*4. These results showed that nuclear DNA polymorphism analysis is useful, in addition to mtDNA haplotype assay, to detect "Inobuta" having the European genotype from Japanese wild boar populations.     

Electrophoretic polymorphism of erythrocyte leucine aminopeptidase in the wild boar, Sus scrofa

An erythrocyte leucine aminopeptidase (Rbc LAP) electrophoretic polymorphism was detected in Italian wild boars, Sus scrofa. Such a polymorphism has not previously been reported in the domestic pig. It is suggested that this locus could be a marker for genetic differences between the domestic and the wild forms of Sus scrofa.