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Hlongwane NL, Dzomba EF, Hadebe K, van der Nest MA, Pierneef R, Muchadeyi FC. Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations. Animals (Basel) 2024; 14:236. [PMID: 38254405 PMCID: PMC10812692 DOI: 10.3390/ani14020236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/17/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer's extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the identified regions included quantitative loci (QTLs) associated with economically important traits. For example, meat and carcass QTLs were prevalent in all the populations, showing the potential of village and indigenous populations' ability to be managed and improved for such traits. Results of this study therefore increase our understanding of the intricate interplay between selection pressures, genomic adaptations, and desirable traits within South African pig populations.
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Affiliation(s)
- Nompilo L. Hlongwane
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, South Africa;
| | - Edgar F. Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville 3209, South Africa;
| | - Khanyisile Hadebe
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
| | - Magriet A. van der Nest
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
- Hans Merensky Chair in Avocado Research, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa;
| | - Rian Pierneef
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa
| | - Farai C. Muchadeyi
- Agricultural Research Council, Biotechnology Platform, Private Bag X5, Onderstepoort 0110, South Africa; (K.H.); (R.P.); (F.C.M.)
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Figueroa CE, Mac Allister ME, Acosta DB, Fernández GP, Merino ML. Genetic characterization of domestic pigs in the core zone of swine production of Argentina. Trop Anim Health Prod 2023; 56:20. [PMID: 38110670 DOI: 10.1007/s11250-023-03852-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/20/2023]
Abstract
Argentina is a small player in the global pork market, contributing only 0.7% of the total production. With increasing global demand for meat, there is an opportunity for countries with an agricultural profile to grow their pork production. However, there is a need to understand the current state of the pork production sector in all aspects to inform decision-making. The aim of this study was to genetically characterize pig herds from different production strata in the primary region for pork production in the country. For this purpose, phylogenetic and genetic variability analyses were performed using the mitochondrial control region marker (n=95 pig samples). Moreover, genotyping of ryr1 and PRKAG3 genes (n=108 pig samples) were performed to evaluate the frequency of deleterious alleles for meat quality traits in the region. The results showed high levels of genetic variability in the pig herds (Hd= 0.840 ± 0.031 and π= 0.010 ± 0.001), with a creole sow and Iberian lineage standing out in the phylogeny. The genotyping of the ryr1 marker revealed the presence of the deleterious t allele in all analyzed strata. However, the RN-allele of the PRKAG3 gene was detected only in the two lower strata. This study represents the first analysis of the phylogenetic relationships among domestic pigs from Argentina and provides an initial assessment of genetic variability in the region. Additionally, the results present, for the first time, the frequency of deleterious alleles for pig production in the productive core area, demonstrating their prevalence.
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Affiliation(s)
- C E Figueroa
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires - CIC/Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) UNNOBA-UNSAdA-CONICET, Pergamino, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad autónoma de Buenos Aires, Argentina
| | - M E Mac Allister
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires - CIC/Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) UNNOBA-UNSAdA-CONICET, Pergamino, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad autónoma de Buenos Aires, Argentina
| | - D B Acosta
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires - CIC/Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) UNNOBA-UNSAdA-CONICET, Pergamino, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad autónoma de Buenos Aires, Argentina
| | - G P Fernández
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires - CIC/Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) UNNOBA-UNSAdA-CONICET, Pergamino, Buenos Aires, Argentina
| | - M L Merino
- Centro de Bioinvestigaciones (CeBio), Universidad Nacional del Noroeste de la Provincia de Buenos Aires - CIC/Centro de Investigaciones y Transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) UNNOBA-UNSAdA-CONICET, Pergamino, Buenos Aires, Argentina.
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICPBA), La Plata, Buenos Aires, Argentina.
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Doan K, Schnitzler A, Preston F, Griggo C, Lang G, Belhaoues F, Blaise E, Crégut-Bonnoure E, Frère S, Foucras S, Gardeisen A, Laurent A, Müller W, Picavet R, Puissant S, Yvinec JH, Pilot M. Evolutionary history of the extinct wolf population from France in the context of global phylogeographic changes throughout the Holocene. Mol Ecol 2023; 32:4627-4647. [PMID: 37337956 DOI: 10.1111/mec.17054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 05/20/2023] [Accepted: 06/05/2023] [Indexed: 06/21/2023]
Abstract
Phylogeographic patterns in large mammals result from natural environmental factors and anthropogenic effects, which in some cases include domestication. The grey wolf was once widely distributed across the Holarctic, but experienced phylogeographic shifts and demographic declines during the Holocene. In the 19th-20th centuries, the species became extirpated from large parts of Europe due to direct extermination and habitat loss. We reconstructed the evolutionary history of the extinct Western European wolves based on the mitogenomic composition of 78 samples from France (Neolithic-20th century) in the context of other populations of wolves and dogs worldwide. We found a close genetic similarity of French wolves from ancient, medieval and recent populations, which suggests the long-term continuity of maternal lineages. MtDNA haplotypes of the French wolves showed large diversity and fell into two main haplogroups of modern Holarctic wolves. Our worldwide phylogeographic analysis indicated that haplogroup W1, which includes wolves from Eurasia and North America, originated in Northern Siberia. Haplogroup W2, which includes only European wolves, originated in Europe ~35 kya and its frequency was reduced during the Holocene due to an expansion of haplogroup W1 from the east. Moreover, we found that dog haplogroup D, currently restricted to Europe and the Middle East, was nested within the wolf haplogroup W2. This suggests European origin of haplogroup D, probably as a result of an ancient introgression from European wolves. Our results highlight the dynamic evolutionary history of European wolves during the Holocene, with a partial lineage replacement and introgressive hybridization with local dog populations.
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Affiliation(s)
- Karolina Doan
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Annik Schnitzler
- UMR 7194 HNHP CNRS/MNHN/UPVD, Equipe NOMADE, Muséum national d'histoire naturelle, Paris, France
| | | | - Christophe Griggo
- Université Grenoble Alpes, Laboratoire EDYTEM, URM 5204 Bâtiment "Pôle Montagne", 5 bd de la mer Caspienne, France
| | - Gérard Lang
- Espace Chasse et Nature Chemin de Strasbourg, France
| | - Fabien Belhaoues
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Emilie Blaise
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | - Evelyne Crégut-Bonnoure
- Muséum Requien, Avignon; Laboratoire TRACES-UMR 5608, Université Toulouse-Jean Jaurès, Toulouse, France
| | - Stéphane Frère
- Inrap, UMR 7209 AASPE, Muséum National d'Histoire Naturelle, La Courneuve, France
| | | | - Armelle Gardeisen
- ASM - Archéologie des Sociétés Méditerranéennes, UMR 5140, Université Paul-Valéry, CNRS, MCC, Montpellier, France
- Labex ARCHIMEDE programme IA-ANR-11-LABX-0032-01, Montpellier, France
| | | | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Avenue de Bellevaux 51, Neuchâtel, Switzerland
| | | | - Stéphane Puissant
- Muséum d'Histoire naturelle - Jardin de l'Arquebuse CS 73310 F-21033 Dijon Cedex, France
| | - Jean-Hervé Yvinec
- INRAP, UMR 7209 AASPE, Laboratoire d'archéozoologie de Compiègne, CRAVO, Compiègne, France
| | - Małgorzata Pilot
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
- School of Life Sciences, University of Lincoln, Lincoln, UK
- Faculty of Biology, University of Gdańsk, Gdańsk, Poland
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Razmaitė V, Šiukščius A, Marašinskienė Š. Cranial Morphology of Lithuanian Indigenous Wattle Pigs and Their Hybrids with Wild Boar. Animals (Basel) 2023; 13:ani13091453. [PMID: 37174490 PMCID: PMC10177289 DOI: 10.3390/ani13091453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/12/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
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.
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Affiliation(s)
- Violeta Razmaitė
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
| | - Artūras Šiukščius
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
| | - Šarūnė Marašinskienė
- Department of Animal Breeding and Reproduction, Animal Science Institute, Lithuanian University of Health Sciences, R. Žebenkos 12, 82317 Baisogala, Lithuania
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5
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Gethöffer F, Keuling O, Maistrelli C, Ludwig T, Siebert U. Heavy Youngsters-Habitat and Climate Factors Lead to a Significant Increase in Body Weight of Wild Boar Females. Animals (Basel) 2023; 13:ani13050898. [PMID: 36899755 PMCID: PMC10000140 DOI: 10.3390/ani13050898] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
As one of the most abundant game species in Europe, European wild boar (Sus scrofa) populations prove highly adaptable to cultivated landscapes. The ongoing process of climate change and the high agricultural yields seem to further optimize the living conditions for this species. In long-term reproduction monitoring, we collected data on the body weight of wild boar females. Over an 18-year period, the body weight of wild boar females increased continuously, then stopped and decreased. It was possible to detect differences between the body weights of animals from forest and agricultural areas. For these areas, differences in body weight development also led to a significant distinction in the onset of puberty. We conclude that, even in a highly cultivated landscape, forested areas provide habitat characteristics that may strongly influence reproduction. Second, with dominant agricultural areas in Germany, wild boar reproduction has been favored in recent decades.
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Spatial genetic structure of European wild boar, with inferences on late-Pleistocene and Holocene demographic history. Heredity (Edinb) 2023; 130:135-144. [PMID: 36639700 PMCID: PMC9981775 DOI: 10.1038/s41437-022-00587-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023] Open
Abstract
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.
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7
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Zanni M, Brogi R, Merli E, Apollonio M. The wolf and the city: insights on wolves conservation in the anthropocene. Anim Conserv 2023. [DOI: 10.1111/acv.12858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Affiliation(s)
- M. Zanni
- Department of Veterinary Medicine University of Sassari Sassari Italy
| | - R. Brogi
- Department of Veterinary Medicine University of Sassari Sassari Italy
| | - E. Merli
- Department of Veterinary Medicine University of Sassari Sassari Italy
| | - M. Apollonio
- Department of Veterinary Medicine University of Sassari Sassari Italy
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8
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Bilbija B, Spitzweg C, Papoušek I, Fritz U, Földvári G, Mullett M, Ihlow F, Sprong H, Civáňová Křížová K, Anisimov N, Belova OA, Bonnet SI, Bychkova E, Czułowska A, Duscher GG, Fonville M, Kahl O, Karbowiak G, Kholodilov IS, Kiewra D, Krčmar S, Kumisbek G, Livanova N, Majláth I, Manfredi MT, Mihalca AD, Miró G, Moutailler S, Nebogatkin IV, Tomanović S, Vatansever Z, Yakovich M, Zanzani S, Široký P. Dermacentor reticulatus - a tick on its way from glacial refugia to a panmictic Eurasian population. Int J Parasitol 2023; 53:91-101. [PMID: 36549441 DOI: 10.1016/j.ijpara.2022.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 10/26/2022] [Accepted: 11/04/2022] [Indexed: 12/23/2022]
Abstract
The ornate dog tick (Dermacentor reticulatus) shows a recently expanding geographic distribution. Knowledge on its intraspecific variability, population structure, rate of genetic diversity and divergence, including its evolution and geographic distribution, is crucial to understand its dispersal capacity. All such information would help to evaluate the potential risk of future spread of associated pathogens of medical and veterinary concern. A set of 865 D. reticulatus ticks was collected from 65 localities across 21 countries, from Portugal in the west to Kazakhstan and southern Russia in the east. Cluster analyses of 16 microsatellite loci were combined with nuclear (ITS2, 18S) and mitochondrial (12S, 16S, COI) sequence data to uncover the ticks' population structures and geographical patterns. Approximate Bayesian computation was applied to model evolutionary relationships among the found clusters. Low variability and a weak phylogenetic signal showing an east-west cline were detected both for mitochondrial and nuclear sequence markers. Microsatellite analyses revealed three genetic clusters, where the eastern and western cluster gradient was supplemented by a third, northern cluster. Alternative scenarios could explain such a tripartite population structure by independent formation of clusters in separate refugia, limited gene flow connected with isolation by distance causing a "bipolar pattern", and the northern cluster deriving from admixture between the eastern and western populations. The best supported demographic scenario of this tick species indicates that the northern cluster derived from admixture between the eastern and western populations 441 (median) to 224 (mode) generations ago, suggesting a possible link with the end of the Little Ice Age in Europe.
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Affiliation(s)
- Branka Bilbija
- Department of Biology and Wildlife Diseases, FVHE, University of Veterinary Sciences Brno, Palackého 1946/1, 61242 Brno, Czech Republic
| | - Cäcilia Spitzweg
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Ivo Papoušek
- Department of Biology and Wildlife Diseases, FVHE, University of Veterinary Sciences Brno, Palackého 1946/1, 61242 Brno, Czech Republic
| | - Uwe Fritz
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Gábor Földvári
- Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Konkoly-Thege Miklós út 29-33, Hungary; Centre for Eco-Epidemiology, National Laboratory for Health Security, 1121 Budapest, Konkoly-Thege Miklós út 29-33, Hungary
| | - Martin Mullett
- Phytophthora Research Centre, Faculty of Forestry and Wood Technology, Department of Forest Protection and Wildlife Management, Mendel University in Brno, Zemědělská 3, 61300 Brno, Czech Republic
| | - Flora Ihlow
- Museum of Zoology, Senckenberg Dresden, A. B. Meyer Building, 01109 Dresden, Germany
| | - Hein Sprong
- National Institute of Public Health and Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Zoonoses and Environmental Microbiology (Z&O), Mailbox 63, room V353, Antonie van Leeuwenhoeklaan 9, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Kristína Civáňová Křížová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, 611 37 Brno, Czech Republic
| | - Nikolay Anisimov
- Institute of Environmental and Agricultural Biology (X-BIO), University of Tyumen, Volodarskogo 6, 625003 Tyumen, Russia
| | - Oxana A Belova
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis) prem. 8, k.17, pos. Institut Poliomyelita, Poselenie Moskovskiy, 108819 Moscow, Russia
| | - Sarah I Bonnet
- Functional Genetics of Infectious Diseases Unit, Institut Pasteur, CNRS UMR 2000, Université de Paris, 75015 Paris, France; Animal Health Department, INRAE, 37380 Nouzilly, France
| | - Elizabeth Bychkova
- Laboratory of Parasitology, State Scientific and Production Association "Scientific and Practical Center of the National Academy of Sciences of Belarus on Bioresources", 27, Akademicheskaya Str, 220072 Minsk, Belarus
| | - Aleksandra Czułowska
- Department of Microbial Ecology and Acaroentomology, Faculty of Biological Sciences, University of Wroclaw, Przybyszewskiego str. 63, 51-148 Wroclaw, Poland
| | - Georg G Duscher
- Department of Pathobiology, Institute of Parasitology, University of Veterinary Medicine Vienna, Vienna, Austria; AGES-Austrian Agency for Health and Food Safety, Spargelfeldstrasse 191, Vienna, 1220, Austria
| | - Manoj Fonville
- National Institute of Public Health and Environment (RIVM), Centre for Infectious Disease Control (CIb), Laboratory for Zoonoses and Environmental Microbiology (Z&O), Mailbox 63, room V353, Antonie van Leeuwenhoeklaan 9, P.O. Box 1, 3720 BA Bilthoven, The Netherlands
| | - Olaf Kahl
- Tick-radar GmbH, 10555 Berlin, Germany
| | - Grzegorz Karbowiak
- Witold Stefański Institute of Parasitology of Polish Academy of Sciences, Twarda street 51/55, 00-818 Warsaw, Poland
| | - Ivan S Kholodilov
- FSASI "Chumakov FSC R&D IBP RAS" (Institute of Poliomyelitis) prem. 8, k.17, pos. Institut Poliomyelita, Poselenie Moskovskiy, 108819 Moscow, Russia
| | - Dorota Kiewra
- Department of Microbial Ecology and Acaroentomology, Faculty of Biological Sciences, University of Wroclaw, Przybyszewskiego str. 63, 51-148 Wroclaw, Poland
| | - Stjepan Krčmar
- Department of Biology, Josip Juraj Strossmayer University of Osijek, Cara Hadrijana 8/A, HR-31000 Osijek, Croatia
| | - Gulzina Kumisbek
- Asfendiyarov Kazakh National Medical University, School of Pharmacy, Department of Engineering Disciplines, Tole Bi, 94, Almaty, Kazakhstan
| | - Natalya Livanova
- Institute of Systematics and Ecology of Animals, Frunze str. 11, Novosibirsk 630091, Russia
| | - Igor Majláth
- Pavol Jozef Safarik University in Kosice, Faculty of Science, Institute of Biology and Ecology, Department of Animal Physiology, Srobarova 2, 041 54 Kosice, Slovakia
| | - Maria Teresa Manfredi
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca, Calea Manastur 3-5, Cluj-Napoca 400372, Romania
| | - Guadalupe Miró
- Animal Health Dept. Veterinary School, Universidad Complutense de Madrid, Spain
| | - Sara Moutailler
- Anses, INRAE, Ecole Nationale Vétérinaire d'Alfort, UMR BIPAR, Laboratoire de Santé Animale, Maisons-Alfort, F-94700, France
| | - Igor V Nebogatkin
- I.I. Schmalhausen Institute of Zoology of National Academy of Sciences of Ukraine, Bogdana Khmelnytskovo 15, 01030 Kyiv, Ukraine; Public Health Center of the Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Snežana Tomanović
- University of Belgrade, Institute for Medical Research, National Institute of Republic of Serbia, Dr. Subotića 4, Belgrade, Serbia
| | - Zati Vatansever
- Kafkas University, Faculty of Veterinary Medicine, Dept. of Parasitology, Kars, Turkey
| | - Marya Yakovich
- Laboratory of Parasitology, State Scientific and Production Association "Scientific and Practical Center of the National Academy of Sciences of Belarus on Bioresources", 27, Akademicheskaya Str, 220072 Minsk, Belarus
| | - Sergio Zanzani
- Department of Veterinary Medicine and Animal Sciences, Università degli Studi di Milano, via dell'Università 6, 26900 Lodi, Italy
| | - Pavel Široký
- Department of Biology and Wildlife Diseases, FVHE, University of Veterinary Sciences Brno, Palackého 1946/1, 61242 Brno, Czech Republic; CEITEC-Central European Institute of Technology, University of Veterinary Sciences Brno, Palackého 1946/1, 612 42 Brno, Czech Republic.
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Frank K, Szepesi K, Bleier N, Sugár L, Kusza S, Barta E, Horn P, Orosz L, Stéger V. Genetic traces of dispersal and admixture in red deer (Cervus elaphus) populations from the Carpathian Basin. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-022-01602-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AbstractAfter the last glacial, the Carpathian Basin was repopulated from either eastward or northward colonisation routes for various species; one of these was the emblematic member of the European megafauna, the red deer, Cervus elaphus. We analysed 303 red deer individuals from the middle of the region, in seven Hungarian game reserves, at ten microsatellite loci (C01, C229, T26, T108, T123, T156, T172, T193, T501, T507), to investigate the genetic diversity of these subpopulations. We discovered high levels of genetic diversity of red deer subpopulations; allelic richness values ranging 4.99–7.01, observed heterozygosity 0.729–0.800, polymorphic information content 0.722–0.806, and Shannon’s information index 1.668–2.064. Multi-locus analyses indicated population admixtures of various degrees that corresponded to geographical location, and complex genetic structures were shown by clustering. Populations in the south-western and the north-eastern parts of the region formed two highly separated groups, and the red deer from populations in between them were highly admixed (in western Pannonia/Transdanubia, where the Danube flows into the Carpathian Basin). This pattern corresponds to the distribution of mitochondrial as well as Y-chromosome lineages. Assignment tests showed that a large fraction of individuals (29.4%) are found outside of their population of origin, indicating that the dispersal of red deer is rather common, which could be expected considering the life course of the species.
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10
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“Guess Who’s Coming to Dinner”: Molecular Tools to Reconstruct multilocus Genetic Profiles from Wild Canid Consumption Remains. Animals (Basel) 2022; 12:ani12182428. [PMID: 36139288 PMCID: PMC9495216 DOI: 10.3390/ani12182428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/05/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Non-invasive genetic sampling is a practical tool to monitor pivotal ecological parameters and population dynamic patterns of endangered species. It can be particularly suitable when applied to elusive carnivores such as the Apennine wolf (Canis lupus italicus) and the European wildcat (Felis silvestris silvestris), which can live in overlapping ecological contexts and sometimes share their habitats with their domestic free-ranging relatives, increasing the risk of anthropogenic hybridisation. In this case study, we exploited all the ecological and genetic information contained in a single biological canid faecal sample, collected in a forested area of central Italy, to detect any sign of trophic interactions between wolves and European wildcats or their domestic counterparts. Firstly, the faecal finding was morphologically examined, showing the presence of felid hair and claw fragment remains. Subsequently, total genomic DNA contained in the hair and claw samples was extracted and genotyped, through a multiple-tube approach, at canid and felid diagnostic panels of microsatellite loci. Finally, the obtained individual multilocus genotypes were analysed with reference wild and domestic canid and felid populations to assess their correct taxonomic status using Bayesian clustering procedures. Assignment analyses classified the genotype obtained from the endothelial cells present on the hair sample as a wolf with slight signals of dog ancestry, showing a qi = 0.954 (C.I. 0.780–1.000) to the wolf cluster, and the genotype obtained from the claw as a domestic cat, showing a qi = 0.996 (95% C.I. = 0.982–1.000) to the domestic cat cluster. Our results clearly show how a non-invasive multidisciplinary approach allows the cost-effective identification of both prey and predator genetic profiles and their taxonomic status, contributing to the improvement of our knowledge about feeding habits, predatory dynamics, and anthropogenic hybridisation risk in threatened species.
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Gong Y, Zhang HY, Yuan Y, He Y, Zhang W, Han Y, Na R, Zeng Y, Luo J, Yang H, Huang Y, Zhao Y, Zhao Z, E GX. Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa. Animals (Basel) 2022; 12:ani12081037. [PMID: 35454283 PMCID: PMC9030587 DOI: 10.3390/ani12081037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/23/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.
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12
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Insights on the historical biogeography of Philippine domestic pigs and its relationship with continental domestic pigs and wild boars. PLoS One 2022; 17:e0254299. [PMID: 35344556 PMCID: PMC8959178 DOI: 10.1371/journal.pone.0254299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
The Philippine archipelago was believed to have never been connected to the Asian continent even during the severe Quaternary sea-level drops. As a result, the history of domestic pig (Sus scrofa) dispersal in the Philippines remains controversial and must have some anthropogenic origin associated with human migration events. In this study, the context of origin, dispersal, and the level of genetic introgression in Philippine domestic pigs were deduced using mitochondrial DNA D-loop analysis altogether with domestic pigs and wild boar corresponding to their geographic origin. The results revealed considerable genetic diversity (0.900±0.016) and widespread Asian pig-ancestry (94.60%) in the phylogenetic analysis, with admixed European pig-origin (5.10%) harboring various fractions of ancestry from Berkshire and Landrace. The close genetic connection between the continental wild boars and domestic pigs present in the Philippine domestic pigs corroborates our hypothesis of a genetic signal that may be associated with the recently reported multiple waves of human migrations to the Philippines. The Haplogroup D7, reported to occur only in Indo-Burma Biodiversity Hotspots, included a high frequency of Philippine domestic pig haplotypes (54.08%), which poses an interesting challenge because its distribution is not consistent with the hypothesized migration route of Neolithic Austronesian-speaking populations. We detected the first Pacific Clade signature and ubiquitously distributed D2 haplotypes (Asian major) on several Philippine islands. The analyses of mismatch distribution and neutrality test were consistent with the Bayesian skyline plot which showed a long stationary period of effective population size. The population decline was consistent with the pronounced population bottleneck in Asian and European pigs during the interglacial periods of the Pleistocene. The results of this study will support the conservation strategies and improvements of economically important genetic resources in the Philippines.
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Figueroa CE, Acosta DB, Mac Allister ME, Merele M, Fernández GP, Carpinetti BN, Winter M, Abate S, Barandiaran S, Merino ML. Patterns of genetic variation on wild pig ( Sus scrofa) populations over a complete range of the species in Argentina. MAMMALIA 2022. [DOI: 10.1515/mammalia-2021-0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
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.
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Affiliation(s)
- Carlos Ezequiel Figueroa
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICPBA)/Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), UNNOBA-UNSAdA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Pergamino , Buenos Aires , Argentina
| | - Diana Belén Acosta
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICPBA)/Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), UNNOBA-UNSAdA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Pergamino , Buenos Aires , Argentina
| | - Matias Exequiel Mac Allister
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICPBA)/Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), UNNOBA-UNSAdA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Pergamino , Buenos Aires , Argentina
| | - Matías Merele
- Universidad Nacional de La Rioja , La Rioja , Argentina
| | - Gabriela Paula Fernández
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICPBA)/Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), UNNOBA-UNSAdA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Pergamino , Buenos Aires , Argentina
| | - Bruno Nicolás Carpinetti
- Gestión Ambiental/Ecología, Instituto de Ciencias Sociales y Administración, Universidad Nacional Arturo Jauretche , Florencio Varela , Buenos Aires , Argentina
| | - Marina Winter
- Universidad Nacional de Río Negro-Sede Atlántica, Centro de Investigaciones y Transferencia Rio Negro (CONICET-UNRN) , Viedma , Río Negro , Argentina
| | - Sergio Abate
- Universidad Nacional de Río Negro-Sede Atlántica, Centro de Investigaciones y Transferencia Rio Negro (CONICET-UNRN) , Viedma , Río Negro , Argentina
| | - Soledad Barandiaran
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Ciudad Autonoma de Buenos Aires , Buenos Aires , Argentina
| | - Mariano Lisandro Merino
- Centro de Bioinvestigaciones, Universidad Nacional del Noroeste de la Provincia de Buenos Aires (UNNOBA-CICPBA)/Centro de Investigaciones y Transferencias del Noroeste de la provincia de Buenos Aires (CITNOBA-CONICET), UNNOBA-UNSAdA, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) , Pergamino , Buenos Aires , Argentina
- Comisión de Investigaciones Científicas de la Provincia de Buenos Aires (CICBA) , La Plata , Buenos Aires , Argentina
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Introgressive hybridisation between domestic pigs (Sus scrofa domesticus) and endemic Corsican wild boars (S. s. meridionalis): effects of human-mediated interventions. Heredity (Edinb) 2022; 128:279-290. [PMID: 35273382 PMCID: PMC8986821 DOI: 10.1038/s41437-022-00517-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/17/2022] Open
Abstract
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.
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15
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Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
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16
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Clear phylogeographic pattern and genetic structure of wild boar Sus scrofa population in Central and Eastern Europe. Sci Rep 2021; 11:9680. [PMID: 33958636 PMCID: PMC8102581 DOI: 10.1038/s41598-021-88991-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/19/2021] [Indexed: 11/15/2022] Open
Abstract
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.
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17
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Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes. Mol Ecol Resour 2021; 21:2369-2387. [PMID: 33942522 DOI: 10.1111/1755-0998.13411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.
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Affiliation(s)
- Evy Arida
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hadi Dahruddin
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Yuli Sulistya Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir Hamidy
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Awal Riyanto
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Sigit Wiantoro
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Moch Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Renny K Hadiaty
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Apandi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Frengky Krey
- Jurusan Perikanan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Papua, Jl. Gunung Salju Amban, Manokwari, Indonesia
| | - Kurnianingsih
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Edy H P Melmambessy
- Program Studi Manajemen Sumberdaya Perairan, Fakultas Pertanian, Universitas Musamus, Jl. Kamizaun Mopah Lama, Rimba Jaya, Merauke, Indonesia
| | - Mulyadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Henderite L Ohee
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Saidin
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Ayub Salamuk
- Dinas Kelautan dan Perikanan Kabupaten Kaimana, Jl.Utarum Kampung Coa, Kaimana, Indonesia
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Nanang Supriatna
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir M Suruwaky
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Wahyudi Tri Laksono
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Evie L Warikar
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Hadi Wikanta
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Aksamina M Yohanita
- Jurusan Biologi, Fakultas MIPA, Universitas Papua Jl. Gunung Salju - Amban, Manokwari, Indonesia
| | - Jacques Slembrouck
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Marc Legendre
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Philippe Gaucher
- USR LEEISA- Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens, Centre de Recherche de Montabo, cayenne, French Guiana
| | - Christophe Cochet
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | | | | | - Borja Mila
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Antoine Fouquet
- UMR 5174 EDB CNRS, Université Paul Sabatier, IRD, Toulouse, France
| | - Alex Borisenko
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER), Université de Montpellier, Montpellier, France
| | - Gono Semiadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
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Spatial Genetic Structure and Demographic History of the Wild Boar in the Qinling Mountains, China. Animals (Basel) 2021; 11:ani11020346. [PMID: 33572967 PMCID: PMC7912324 DOI: 10.3390/ani11020346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/23/2021] [Accepted: 01/27/2021] [Indexed: 12/04/2022] Open
Abstract
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.
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Barros T, Ferreira E, Rocha RG, Brotas G, Carranza J, Fonseca C, Torres RT. The Multiple Origins of Roe Deer Populations in Western Iberia and Their Relevance for Conservation. Animals (Basel) 2020; 10:ani10122419. [PMID: 33348694 PMCID: PMC7765819 DOI: 10.3390/ani10122419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/05/2020] [Accepted: 12/14/2020] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The Iberian Peninsula is considered a reservoir of genetic diversity and the source for the recolonization of continental Europe by several mammal species, after the last glaciation period. Here, we intended to characterize the genetic patterns and origins of one of those species, the roe deer, through the analysis of different genetic markers, as there is a major knowledge gap about the species’ populations at the western edge of roe deer distribution in the Iberian Peninsula. We found that western Iberia is a diversity hotspot for roe deer, with shared gene pools with other European and Iberian regions, but also with unique genetic elements, particularly the case of the relict population of Peneda Gerês National Park. Due to the distinct genetic diversity that was observed in western Iberian populations, we highlight the importance of these populations as sources of resilience against global changes. Our results provide useful information for the management and conservation of this species in the Iberian Peninsula. We advise transboundary management between Portugal and Spain as a rule, as well as careful evaluation of reintroduction actions, that should take in account the genetic data, in order to maintain the genetic heritage of roe deer in Europe. Abstract The roe deer (Capreolus capreolus) is native and widespread in Europe and its phylogeography has been clarified in the last decades. Southern peninsulas are considered as reservoirs of genetic diversity and the source for the recolonization of Europe after the last glacial maximum. Even though roe deer populations have been genetically characterized, there is a major knowledge gap about the populations at the western edge of its distribution. To fill this caveat, and based on mitochondrial and nuclear DNA data, we aim to: (i) characterize the genetic diversity and structure of roe deer in western Iberia; (ii) clarify the origins and phylogeographical affinities of these populations, namely the relict population from Peneda Gerês National Park (PNPG, Portugal) and the likely allochthonous populations from central and south (CS) Portugal; (iii) discuss the implications of our findings for the management and conservation of the roe deer. Three major genetic clusters were inferred based on nuclear genotypes and were structured in a similar way as the three major mtDNA clades present in Iberia. Patterns inferred with nuclear markers confirmed PNPG as a relict population. Roe deer from CS Portugal share haplotypes with Central Europe rather than with other western Iberian populations, confirming its mainly allochthonous origin. Our results highlight western Iberia as a diversity hotspot for roe deer. We highlight the role of intraspecific genetic diversity as a source of resilience against ongoing global changes; the need for transboundary management and the importance of genetic data to inform management and conservation. When considered, repopulation or translocation measures should follow the IUCN Law of Reintroductions and meticulously conducted in order to preserve the genetic heritage of the species.
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Affiliation(s)
- Tânia Barros
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar), Campus Universitário Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (T.B.); (C.F.); (R.T.T.)
| | - Eduardo Ferreira
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar), Campus Universitário Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (T.B.); (C.F.); (R.T.T.)
- Correspondence:
| | - Rita Gomes Rocha
- CIBIO-InBIO (Centro de Investigação em Biodiversidade e Recursos Genéticos), Campus de Vairão, Universidade do Porto, 4485-661 Vairão, Portugal;
| | - Gonçalo Brotas
- ACHLI (Associação de Conservação do Habitat do Lobo Ibérico), Rua 25 de Abril 37, 4740-002 Esposende, Portugal;
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), Campus de Rabanales, Universidad de Córdoba, Colonia San José, 94560 Córdoba, Spain;
| | - Carlos Fonseca
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar), Campus Universitário Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (T.B.); (C.F.); (R.T.T.)
- ForestWISE—Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Rita Tinoco Torres
- Departamento de Biologia & CESAM (Centro de Estudos do Ambiente e do Mar), Campus Universitário Santiago, Universidade de Aveiro, 3810-193 Aveiro, Portugal; (T.B.); (C.F.); (R.T.T.)
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Nayfa MG, Jones DB, Benzie JAH, Jerry DR, Zenger KR. Comparing Genomic Signatures of Selection Between the Abbassa Strain and Eight Wild Populations of Nile Tilapia ( Oreochromis niloticus) in Egypt. Front Genet 2020; 11:567969. [PMID: 33193660 PMCID: PMC7593532 DOI: 10.3389/fgene.2020.567969] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 08/31/2020] [Indexed: 11/16/2022] Open
Abstract
Domestication to captive rearing conditions, along with targeted selective breeding have genetic consequences that vary from those in wild environments. Nile tilapia (Oreochromis niloticus) is one of the most translocated and farmed aquaculture species globally, farmed throughout Asia, North and South America, and its African native range. In Egypt, a breeding program established the Abbassa Strain of Nile tilapia (AS) in 2002 based on local broodstock sourced from the Nile River. The AS has been intensively selected for growth and has gone through genetic bottlenecks which have likely shifted levels and composition of genetic diversity within the strain. Consequently, there are questions on the possible genetic impact AS escapees may have on endemic populations of Nile tilapia. However, to date there have been no genetic studies comparing genetic changes in the domesticated AS to local wild populations. This study used 9,827 genome-wide SNPs to investigate population genetic structure and signatures of selection in the AS (generations 9–11) and eight wild Nile tilapia populations from Egypt. SNP analyses identified two major genetic clusters (captive and wild populations), with wild populations showing evidence of isolation-by-distance among the Nile Delta and upstream riverine populations. Between genetic clusters, approximately 6.9% of SNPs were identified as outliers with outliers identified on all 22 O. niloticus chromosomes. A lack of localized outlier clustering on the genome suggests that no genes of major effect were presently detected. The AS has retained high levels of genetic diversity (Ho_All = 0.21 ± 0.01; He_All = 0.23 ± 0.01) when compared to wild populations (Ho_All = 0.18 ± 0.01; He_All = 0.17 ± 0.01) after 11 years of domestication and selective breeding. Additionally, 565 SNPs were unique within the AS line. While these private SNPs may be due to domestication signals or founder effects, it is suspected that introgression with blue tilapia (Oreochromis aureus) has occurred. This study highlights the importance of understanding the effects of domestication in addition to wild population structure to inform future management and dissemination decisions. Furthermore, by conducting a baseline genetic study of wild populations prior to the dissemination of a domestic line, the effects of aquaculture on these populations can be monitored over time.
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Affiliation(s)
- Maria G Nayfa
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - John A H Benzie
- WorldFish, Penang, Malaysia.,School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| | - Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Centre for Tropical Bioinformatics and Molecular Biology, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
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Mihalik B, Frank K, Astuti PK, Szemethy D, Szendrei L, Szemethy L, Kusza S, Stéger V. Population Genetic Structure of the Wild Boar ( Sus scrofa) in the Carpathian Basin. Genes (Basel) 2020; 11:genes11101194. [PMID: 33066463 PMCID: PMC7602151 DOI: 10.3390/genes11101194] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/06/2020] [Accepted: 10/12/2020] [Indexed: 12/05/2022] Open
Abstract
In the Carpathian Basin the wild boar (Sus scrofa) belongs among the most important game species both ecologically and economically, therefore knowing more about the basics of the genetics of the species is a key factor for accurate and sustainable management of its population. The aim of this study was to estimate the genetic diversity and to elucidate the genetic structure and location of wild boar populations in the Carpathian Basin. A total of 486 samples were collected and genotyped using 13 STR markers. The number of alleles varied between 4 and 14, at 9 of the 13 loci the observed heterozygosity was significantly different (p < 0.05) from the expected value, showing remarkable introgression in the population. The population was separated into two groups, with an Fst value of 0.03, suggesting the presence of two subpopulations. The first group included 147 individuals from the north-eastern part of Hungary, whereas the second group included 339 samples collected west and south of the first group. The two subpopulations’ genetic indices are roughly similar. The lack of physical barriers between the two groups indicates that the genetic difference is most likely caused by the high reproduction rate and large home range of the wild boars, or by some genetic traces’ having been preserved from both the last ice age and the period before the Hungarian water regulation.
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Affiliation(s)
- Bendegúz Mihalik
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032 Debrecen, Hungary; (B.M.); (K.F.); (P.K.A.)
- NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary;
- Doctoral School of Animal Science, University of Debrecen, 4032 Debrecen, Hungary
| | - Krisztián Frank
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032 Debrecen, Hungary; (B.M.); (K.F.); (P.K.A.)
| | - Putri Kusuma Astuti
- Institute of Animal Science, Biotechnology and Nature Conservation, University of Debrecen, 4032 Debrecen, Hungary; (B.M.); (K.F.); (P.K.A.)
| | - Dániel Szemethy
- NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary;
| | - László Szendrei
- Department of Nature Conservation Zoology and Game Management, University of Debrecen, 4032 Debrecen, Hungary;
| | - László Szemethy
- Faculty of Regional Development, University of Pécs, 7100 Szekszárd, Hungary;
| | - Szilvia Kusza
- Animal Genetics Laboratory, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence: (S.K.); (V.S.)
| | - Viktor Stéger
- NARIC Agricultural Biotechnological Institute, 2100 Gödöllő, Hungary;
- Correspondence: (S.K.); (V.S.)
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Historical range expansion and biological changes of Sus scrofa corresponding to domestication and feralization. MAMMAL RES 2020. [DOI: 10.1007/s13364-020-00534-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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23
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Silva EC, McManus C, Piovezan U, Faria DA, Souza CA, Caetano AR, Paiva SR. Phylogeography of feral Monteiro pig in the Brazilian Pantanal Ecosystem. Genetica 2020; 148:183-193. [PMID: 32770285 DOI: 10.1007/s10709-020-00099-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
The Monteiro is a feral pig found in the Brazilian Pantanal ecosystem. The goal of this research is to generate data and knolewdge related to animal populations wich can be used for management and development of an in vitro conservation program for animal resourses at Pantanal ecosystem. The present study evaluated animals sampled from 10 distinct locations within the region, using 19 microsatellite markers (N = 189) and the control region of mitochondrial DNA (mtDNA) (N = 392). Low genetic differences were found between populations with the microsatellite data. The FST range was between 0.009 and 0.063 (p-value < 0.05). The Mantel test corroborated with previous results, as low correlations between genetic and geographic distances were observed (r2 = 0.2309, p = 0.06). Bayesian analysis for genetic structure identification placed the Monteiro pigs into three main clusters (MOB, Pop 1 and all others Pantanal populations). Most of the Monteiro pigs share a single European haplotype as seen by mtDNA analyses. This haplotype is not exclusive, as it is shared with other swine populations (commercial and other locally adapted breeds). Monteiro populations from different geographic locations within Pantanal are not isolated and can be considered as a large unique population. Since animals roam freely to seek food and water, or even due to seasonal flooding of their habitat, the Monteiro populations presented absence of major genetic structure and evidence of high gene flow. These results can be used to create a management plan and in situ and ex situ conservation program for conservation and use of the Monteiro breed in the Pantanal ecosystem.
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Affiliation(s)
- Elizabete C Silva
- Faculdade de Agronomia E Medicina Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasilia, DF, 70910-900, Brazil
| | - Concepta McManus
- Departamento de Ciências Fisiológicas, Instituto de Biologia, Campus Darcy Ribeiro, Universidade de Brasilia, Asa Norte, Brasilia, DF, 70910-900, Brazil
| | - Ubiratan Piovezan
- Embrapa Tabuleiros Costeiros, Av. Beira Mar, 3250 - Jardins, Aracaju, SE, 49025-040, Brazil
| | - Danielle A Faria
- Faculdade de Agronomia E Medicina Veterinária, Instituto Central de Ciências, Campus Darcy Ribeiro, Universidade de Brasília, Asa Norte, Brasilia, DF, 70910-900, Brazil
| | - Carla A Souza
- La Trobe University, Plenty Rd & Kingsbury Dr., Bundoora, VIC, 3086, Australia
| | - Alexandre R Caetano
- Embrapa Recursos Genéticos E Biotecnologia, Final W5 Norte, Brasília, DF, 70770-917, Brazil
| | - Samuel R Paiva
- Embrapa Recursos Genéticos E Biotecnologia, Final W5 Norte, Brasília, DF, 70770-917, Brazil.
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Hu C, Pan T, Wu Y, Zhang C, Chen W, Chang Q. Spatial genetic structure and historical demography of East Asian wild boar. Anim Genet 2020; 51:557-567. [PMID: 32510675 DOI: 10.1111/age.12955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/21/2020] [Accepted: 05/01/2020] [Indexed: 11/30/2022]
Abstract
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.
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Affiliation(s)
- C Hu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - T Pan
- School of Life Sciences, Anhui Normal University, Wuhu, Anhui, 230039, China
| | - Y Wu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
| | - C Zhang
- Faculty of Life Science and Chemical Engineering, Jiangsu Second Normal University, Nanjing, Jiangsu, 210013, China
| | - W Chen
- College of Environment and Ecology, Jiangsu Open University (The City Vocational College of Jiangsu), Nanjing, Jiangsu, 210036, China
| | - Q Chang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu, 210046, China
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Hlongwane NL, Hadebe K, Soma P, Dzomba EF, Muchadeyi FC. Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa. Front Genet 2020; 11:344. [PMID: 32457791 PMCID: PMC7221027 DOI: 10.3389/fgene.2020.00344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.
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Affiliation(s)
- Nompilo Lucia Hlongwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Pranisha Soma
- Animal Production Institute, Agricultural Research Council, Irene, South Africa
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
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Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
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Lorenzini R, Fanelli R, Tancredi F, Siclari A, Garofalo L. Matching STR and SNP genotyping to discriminate between wild boar, domestic pigs and their recent hybrids for forensic purposes. Sci Rep 2020; 10:3188. [PMID: 32081854 PMCID: PMC7035276 DOI: 10.1038/s41598-020-59644-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/13/2020] [Indexed: 11/09/2022] Open
Abstract
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.
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Affiliation(s)
- Rita Lorenzini
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Via Tancia 21, 02100, Rieti, Italy.
| | - Rita Fanelli
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Via Tancia 21, 02100, Rieti, Italy
| | - Francesco Tancredi
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Via Tancia 21, 02100, Rieti, Italy
| | - Antonino Siclari
- Ente Parco Nazionale dell'Aspromonte, Via Aurora 1, 89057 Gambarie di S. Stefano in Aspromonte, Reggio Calabria, Italy
| | - Luisa Garofalo
- Istituto Zooprofilattico Sperimentale delle Regioni Lazio e Toscana "M. Aleandri", Centro di Referenza Nazionale per la Medicina Forense Veterinaria, Via Tancia 21, 02100, Rieti, Italy
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Khederzadeh S, Kusza S, Huang C, Markov N, Scandura M, Babaev E, Šprem N, Seryodkin IV, Paule L, Esmailizadeh A, Xie H, Zhang Y. Maternal genomic variability of the wild boar ( Sus scrofa) reveals the uniqueness of East-Caucasian and Central Italian populations. Ecol Evol 2019; 9:9467-9478. [PMID: 31534669 PMCID: PMC6745674 DOI: 10.1002/ece3.5415] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/03/2019] [Accepted: 06/05/2019] [Indexed: 01/01/2023] Open
Abstract
The phylogeography of the European wild boar was mainly determined by postglacial recolonization patterns from Mediterranean refugia after the last ice age. Here we present the first analysis of SNP polymorphism within the complete mtDNA genome of West Russian (n = 8), European (n = 64), and North African (n = 5) wild boar. Our analyses provided evidence of unique lineages in the East-Caucasian (Dagestan) region and in Central Italy. A phylogenetic analysis revealed that these lineages are basal to the other European mtDNA sequences. We also show close connection between the Western Siberian and Eastern European populations. Also, the North African samples were clustered with the Iberian population. Phylogenetic trees and migration modeling revealed a high proximity of Dagestan sequences to those of Central Italy and suggested possible gene flow between Western Asia and Southern Europe which was not directly related to Northern and Central European lineages. Our results support the presence of old maternal lineages in two Southern glacial refugia (i.e., Caucasus and the Italian peninsula), as a legacy of an ancient wave of colonization of Southern Europe from an Eastern origin.
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Affiliation(s)
- Saber Khederzadeh
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Szilvia Kusza
- Animal Genetics Laboratory, Faculty of Agricultural and Food Sciences and Environmental ManagementUniversity of DebrecenDebrecenHungary
| | - Cui‐Ping Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Nickolay Markov
- Department of Game Animals' Ecology, Institute of Plant and Animal EcologyUral Branch of Russian Academy of SciencesYekaterinburgRussia
| | - Massimo Scandura
- Department of Veterinary MedicineUniversity of SassariSassariItaly
| | - Elmar Babaev
- Caspian Institute of Biological ResourcesMakhachkalaRussia
| | - Nikica Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of AgricultureUniversity of ZagrebZagrebCroatia
| | - Ivan V. Seryodkin
- Pacific Geographical Institute FEB RASVladivostokRussia
- Far Eastern Federal UniversityVladivostokRussia
| | - Ladislav Paule
- Faculty of ForestryTechnical University in ZvolenZvolenSlovakia
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of AgricultureShahid Bahonar University of KermanKermanIran
| | - Hai‐Bing Xie
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Ya‐Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
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Mattucci F, Galaverni M, Lyons LA, Alves PC, Randi E, Velli E, Pagani L, Caniglia R. Genomic approaches to identify hybrids and estimate admixture times in European wildcat populations. Sci Rep 2019; 9:11612. [PMID: 31406125 PMCID: PMC6691104 DOI: 10.1038/s41598-019-48002-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 07/25/2019] [Indexed: 12/22/2022] Open
Abstract
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.
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Affiliation(s)
- Federica Mattucci
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy.
| | | | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, USA
| | - Paulo C Alves
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio - Laboratório Associado, Campus Agrário de Vairão, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, University of Montana, Missoula, USA
| | - Ettore Randi
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Department of Chemistry and Bioscience, Faculty of Engineering and Science, University of Aalborg, Aalborg, Denmark
| | - Edoardo Velli
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
| | - Luca Pagani
- Dipartimento di Biologia, Università degli Studi di Padova, Padua, Italy
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Romolo Caniglia
- Area per la Genetica della Conservazione (BIO-CGE), Istituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA), Ozzano dell'Emilia, Italy
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30
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Anderson D, Toma R, Negishi Y, Okuda K, Ishiniwa H, Hinton TG, Nanba K, Tamate HB, Kaneko S. Mating of escaped domestic pigs with wild boar and possibility of their offspring migration after the Fukushima Daiichi Nuclear Power Plant accident. Sci Rep 2019; 9:11537. [PMID: 31395920 PMCID: PMC6687819 DOI: 10.1038/s41598-019-47982-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/25/2019] [Indexed: 12/03/2022] Open
Abstract
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.
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Affiliation(s)
- Donovan Anderson
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan
| | - Rio Toma
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan
| | - Yuki Negishi
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan
| | - Kei Okuda
- Hiroshima Shudo University, Faculty of Human Environmental Studies, Hiroshima, 731-3195, Japan
| | - Hiroko Ishiniwa
- Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan
| | - Thomas G Hinton
- Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan
| | - Kenji Nanba
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan.,Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan
| | | | - Shingo Kaneko
- Fukushima University, Symbiotic Systems Science and Technology, Fukushima, 960-1248, Japan. .,Fukushima University, Institute of Environmental Radioactivity, Fukushima, 960-1248, Japan.
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31
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Mitochondrial Diversity of the East Balkan Swine (Sus scrofa f. domestica) in South-Eastern Bulgaria. ACTA VET-BEOGRAD 2019. [DOI: 10.2478/acve-2019-0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Abstract
The East Balkan Swine (EBS) is the only preserved local swine breed in Bulgaria and one of the few indigenous pig breeds in Europe. The EBS is distributed in the region of Eastern Balkan Mountains and the Strandja Mountain. To reveal the breed’s genetic profile, we analyzed 50 purebred individuals according to mitochondrial DNA (D-loop region, HVR1) and sequence analysis in the Scientific Center of Agriculture (Sredets region) in the country.
The obtained results show the presence of four haplotypes: three Asian specific haplotypes (H1, H2, and H3) and the European specific E1a1. The haplotypes H2 (6 %) and H3 (2 %) were newly described and were branched from the basic clade H1 (90 %). All haplotypes belong to the Asiatic clade A (98 %), except one sample assigned to the European haplogroup E1 (2 %) in contrast to samples from East North Bulgaria where Asiatic and Europen clades were with almost equal distribution. The coexistence of two mtDNA clades in EBS in Bulgaria may be related to the source of the pig populations and/or the historical crossbreeding with imported pigs.
In conclusion, due to its native origin, the East Balkan Swine may be the only possible option for a solution to the exhaustion of the beneficial genetic variation of available cultural breeds. With its participation, high-productive populations can be restored and established after a long and purposeful selection.
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32
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Phylogeography and epidemiology of Brucella suis biovar 2 in wildlife and domestic swine. Vet Microbiol 2019; 233:68-77. [PMID: 31176415 DOI: 10.1016/j.vetmic.2019.04.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 04/17/2019] [Accepted: 04/18/2019] [Indexed: 11/22/2022]
Abstract
Swine brucellosis due to Brucella suis biovar 2 (bv2) is enzootic in wild boar and hare in continental Europe and may cause major economic losses to the pig industry, mainly in free-ranged pig farms. The high nucleotide identity found among the B. suis biovar 2 isolates has long hindered the full understanding of the epidemiology and the phylogeography of the disease. Here, we used multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) and whole-genome analysis to identify single-nucleotide polymorphisms (SNPs) in order to gain insights from the largest B. suis bv2 dataset analyzed so far composed of domestic pigs and wildlife isolates collected throughout Europe since the 1970s. We found four major clades with a specific phylogeographic pattern. The Iberian clade contains isolates exclusively from the Iberian Peninsula. The Central European clade includes most isolates from France, Northern Italy, Switzerland and an important proportion of those of Northern Spain. The Eastern European clade clustered isolates from Croatia and Hungary mainly but also from areas of France, Germany, Italy and Poland. Finally, a separated Sardinian clade grouped three isolates from this island. At fine scale, MLVA demonstrated an endemic status of the infection in Europe and it allowed tracking a large outbreak formed by different farms from Spain linked to the same infection source. The whole genome SNP analysis showed that the strains form genetically distinct clades, shared between wild boar and pigs, in agreement with the MLVA clades. Interestingly, all hare isolates clustered together within two groups composed exclusively of wildlife isolates. Our results support the hypothesis that maintenance and spread of B. suis bv2 in Europe is a dynamic process linked to the natural expansion of wild boar as the main wild reservoir of the infection, while spread over long distances is found largely dependent on anthropogenic activities.
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Arbanasić H, Konjević D, Vranković L, Bujanić M, Stipoljev S, Balažin M, Šprem N, Škorić D, Galov A. Evolution of MHC class II SLA-DRB1 locus in the Croatian wild boar (Sus scrofa) implies duplication and weak signals of positive selection. Anim Genet 2018; 50:33-41. [PMID: 30357873 DOI: 10.1111/age.12734] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/04/2018] [Indexed: 12/22/2022]
Abstract
The wild boar is an ancestor of the domestic pig and an important game species with the widest geographical range of all ungulates. Although a large amount of data are available on major histocompatibility complex (MHC) variability in domestic pigs, only a few studies have been performed on wild boars. Due to their crucial role in appropriate immune responses and extreme polymorphism, MHC genes represent some of the best candidates for studying the processes of adaptive evolution. Here, we present the results on the variability and evolution of the entire MHC class II SLA-DRB1 locus exon 2 in 133 wild boars from Croatia. Using direct sequencing and cloning methods, we identified 20 SLA-DRB1 alleles, including eight new variants, with notable divergence. In some individuals, we documented functional locus duplication, and SLA-DRB1*04:10 was identified as the allele involved in the duplication. The expression of a duplicated locus was confirmed by cloning and sequencing cDNA-derived amplicons. Based on individual genotypes, we were able to assume that alleles SLA-DRB1*04:10 and SLA-DRB1*06:07 are linked as an allelic combination that co-evolves as a two-locus haplotype. Our investigation of evolutionary processes at the SLA-DRB1 locus confirmed the role of intralocus recombination in generating allelic variability, whereas tests of positive selection based on the dN/dS (non-synonymous/synonymous substitution rate ratio) test revealed atypically weak and ambiguous signals.
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Affiliation(s)
- H Arbanasić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - D Konjević
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - L Vranković
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - M Bujanić
- Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10000, Zagreb, Croatia
| | - S Stipoljev
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - M Balažin
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, 10000, Zagreb, Croatia
| | - D Škorić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - A Galov
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
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34
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Inferring the origin and genetic diversity of the introduced wild boar (Sus scrofa) populations in Argentina: an approach from mitochondrial markers. MAMMAL RES 2018. [DOI: 10.1007/s13364-018-0380-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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35
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Yamazaki Y. Genetic Population Structure of Sika Deer, Cervus nippon, Derived from Multiple Origins, Around Toyama Prefecture of Japan. Zoolog Sci 2018; 35:215-221. [PMID: 29882493 DOI: 10.2108/zs170187] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Recently, expansion of the number and distribution of sika deer, Cervus nippon, in the Japanese Archipelago has resulted in the disturbance of indigenous gene pools and ecosystems. There are also concerns that the artificial introduction of sika deer to certain areas may aggravate this situation. In order to contribute to the conservation of ecosystems, I examined the current state of genetic disturbance and dispersal routes in the sika deer populations around Toyama Prefecture, one of the main areas of expanding sika deer distribution. Of 12 haplotypes detected by mitochondrial DNA D-loop sequence analysis, 10 were found to belong to a previously detected sika deer group in northern Japan, although the remaining two haplotypes corresponded to the southern Japanese sika deer group. The latter two haplotypes were detected at especially high frequencies in the southern area of Toyama Prefecture, suggesting that these haplotypes may derive from artificially introduced individuals. Occurrence patterns of indigenous haplotypes around Toyama Prefecture revealed immigration into Toyama Prefecture through different routes, mainly in the east and south-west. The genetic results presented here may have application in predicting future dispersal routes, as well as aid in the establishment of effective measures for management of sika deer.
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Affiliation(s)
- Yuji Yamazaki
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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36
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Chen J, Lin G, Qin W, Yan J, Zhang T, Su J. The roles of calving migration and climate change in the formation of the weak genetic structure in the Tibetan antelope (Pantholops hodgsonii). Integr Zool 2018; 14:248-258. [PMID: 29851262 DOI: 10.1111/1749-4877.12334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Geographical barriers and distance can reduce gene exchange among animals, resulting in genetic divergence of geographically isolated populations. The Tibetan antelope (Pantholops hodgsonii) has a geographical range of approximately 1600 km across the Qinghai-Tibet Plateau, which comprises a series of tall mountains and big rivers. However, previous studies indicate that there is little genetic differentiation among their geographically delineated populations. To better understand the genetic structure of P. hodgsonii populations, we collected 145 samples from the 3 major calving regions, taking into consideration their various calving grounds and migration routes. We used a combination of mitochondrial sequences (Cyt b, ATPase, D-loop and COX I) to investigate the genetic structure and the evolutionary divergence of the populations. Significant, albeit weak, genetic differentiation was detected among the 3 geographical populations. Analysis of the genetic divergence process revealed that the animals gradually entered a period of rapid genetic differentiation approximately 60 000 years ago. The calving migration of P. hodgsonii cannot be the main cause of their weak genetic structure because this cannot fully homogenize the genetic pool. Instead, the geological and climatic events as well as the coupling vegetation succession process during this period have been suggested to greatly contribute to the genetic structure and the expansion of genetic diversity.
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Affiliation(s)
- Jiarui Chen
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Gonghua Lin
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Wen Qin
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jingyan Yan
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tongzuo Zhang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
| | - Jianping Su
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, China
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37
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Dzialuk A, Zastempowska E, Skórzewski R, Twarużek M, Grajewski J. High domestic pig contribution to the local gene pool of free-living European wild boar: a case study in Poland. MAMMAL RES 2017. [DOI: 10.1007/s13364-017-0331-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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38
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Tabak MA, Piaggio AJ, Miller RS, Sweitzer RA, Ernest HB. Anthropogenic factors predict movement of an invasive species. Ecosphere 2017. [DOI: 10.1002/ecs2.1844] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Michael A. Tabak
- Center for Epidemiology and Animal Health; USDA/APHIS/Veterinary Services; 2150 Centre Avenue Fort Collins Colorado 80526 USA
| | - Antoinette J. Piaggio
- National Wildlife Research Center; USDA/APHIS/Wildlife Services; 4101 LaPorte Avenue Fort Collins Colorado 80521 USA
| | - Ryan S. Miller
- Center for Epidemiology and Animal Health; USDA/APHIS/Veterinary Services; 2150 Centre Avenue Fort Collins Colorado 80526 USA
| | | | - Holly B. Ernest
- Department of Veterinary Sciences; Program in Ecology; University of Wyoming; 1000 E. University Avenue Laramie Wyoming 80271 USA
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39
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Beugin MP, Baubet E, Dufaure De Citres C, Kaerle C, Muselet L, Klein F, Queney G. A set of 20 multiplexed single nucleotide polymorphism (SNP) markers specifically selected for the identification of the wild boar (Sus scrofa scrofa) and the domestic pig (Sus scrofa domesticus). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0738-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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40
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Caliebe A, Nebel A, Makarewicz C, Krawczak M, Krause-Kyora B. Insights into early pig domestication provided by ancient DNA analysis. Sci Rep 2017; 7:44550. [PMID: 28300151 PMCID: PMC5353713 DOI: 10.1038/srep44550] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/09/2017] [Indexed: 11/24/2022] Open
Abstract
Pigs (Sus scrofa) were first domesticated between 8,500 and 8,000 cal BC in the Near East, from where they were subsequently brought into Europe by agriculturalists. Soon after the arrival of the first domestic pigs in northern Europe (~4500 BC), farmers are thought to have started to incorporate local wild boars into their swine herds. This husbandry strategy ultimately resulted in the domestication of European wild boars. Here, we set out to provide a more precise geographic and temporal framework of the early management of suid populations in northern Europe, drawing upon mitochondrial DNA haplotype data from 116 Neolithic Sus specimens. We developed a quantitative mathematical model tracing the haplotypes of the domestic pigs back to their most likely geographic origin. Our modelling results suggest that, between 5000 and 4000 BC, almost all matrilines in the north originated from domesticated animals from the south of central Europe. In the following period (4000–3000 BC), an estimated 78–100% of domesticates in the north were of northern matrilineal origin, largely from local wild boars. These findings point towards a dramatic change in suid management strategies taking place throughout south-central and northern Europe after 4000 BC.
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Affiliation(s)
- Amke Caliebe
- Institute of Medical Informatics and Statistics, Kiel University, 24105 Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany
| | - Cheryl Makarewicz
- Institute of Prehistoric and Protohistoric Archaeology, Kiel University, 24098 Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University, 24105 Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, 24105 Kiel, Germany.,Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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41
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Veličković N, Ferreira E, Djan M, Ernst M, Obreht Vidaković D, Monaco A, Fonseca C. Demographic history, current expansion and future management challenges of wild boar populations in the Balkans and Europe. Heredity (Edinb) 2016; 117:348-357. [PMID: 27436523 PMCID: PMC5061920 DOI: 10.1038/hdy.2016.53] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/31/2016] [Accepted: 06/08/2016] [Indexed: 02/01/2023] Open
Abstract
Wild boar (Sus scrofa), one of the most widespread wildlife species, has entered a stage of continuous growth in Europe, and could even be considered a pest species. We analysed microsatellite variability in 723 wild boars from across Europe, including the northern Dinaric Balkans. Our aims were: (1) to define the population structure of wild boars in the Balkans and its relation with other European populations; (2) to estimate effective populations sizes, levels of intra- and inter-population diversity, inbreeding migration and gene flow patterns; (3) to test subpopulations for bottlenecks; (4) to interpret these results in light of current knowledge about the demographic history of wild boars in Europe; and (5) to discuss the relevance of these findings for management and conservation. Strong population structuring was observed and 14 subpopulations were revealed. High genetic diversity was found, and besides the well-known identity of the Italian populations of Sardinia and Castelporziano, we bring new insights into other potential relevant, refugial populations such as Littoral Slovenia, South Portugal, North-western Iberia and an entire cluster in the Balkans. There was evidence of gene flow going from these refugial subpopulations towards less peripheral and more admixed subpopulations. Recent population bottlenecks and expansions were detected, mostly in the peninsular refuge subpopulations. The results are consistent with the fluctuations of wild boar numbers in Europe since the beginning of the twentieth century. These results should be taken into account in future conservation and management plans for wild boar populations in Europe.
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Affiliation(s)
- N Veličković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - E Ferreira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - M Djan
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - M Ernst
- Department of Forest Protection and Wildlife Management, Mendel University in Brno, Brno, Czech Republic
| | - D Obreht Vidaković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Novi Sad, Serbia
| | - A Monaco
- Regional Parks Agency–Lazio Region, Rome, Italy
| | - C Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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42
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Like a pig out of water: seaborne spread of domestic pigs in Southern Italy and Sardinia during the Bronze and Iron Ages. Heredity (Edinb) 2016; 118:154-159. [PMID: 27649620 DOI: 10.1038/hdy.2016.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022] Open
Abstract
Southern Italy has a long history of human occupation and passage of different cultures since the Early Holocene. Repeated, ancient introductions of pigs in several geographic areas in Europe make it difficult to understand pig translocation and domestication in Italy. The archeozoological record may provide fundamental information on this, hence shedding light on peopling and on trading among different ancient cultures in the Mediterranean. Yet, because of the scanty nature of the fossil record, ancient remains from human-associated animals are somewhat rare. Fortunately, ancient DNA analysis as applied to domestic species proved to be a powerful tool in revealing human migrations. Herein, we analyzed 80-bp fragment of mitochondrial DNA control region from 27 Sus scrofa ancient samples retrieved from Southern Italian and Sardinian archeological sites, spanning in age from the Mesolithic to the Roman period. Our results surprisingly indicate the presence of the Near Eastern haplotype Y1 on both Italy's major islands (Sardinia and Sicily) during the Bronze Age, suggesting the seaborne transportation of domestic pigs by humans at least during 1600-1300 BC. The presence of the Italian E2 clade in domestic contexts shows that the indigenous wild boar was effectively domesticated or incorporated into domestic stocks in Southern Italy during the Bronze Age, although the E2 haplotype has never been found in modern domestic breeds. Pigs belonging to the endemic E2 clade were thus traded between the Peninsula and Sardinia by the end of the second millennium BC and this genetic signature is still detected in Sardinian feral pigs.
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43
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Iacolina L, Brajković V, Canu A, Šprem N, Cubric-Curik V, Fontanesi L, Saarma U, Apollonio M, Scandura M. Novel Y-chromosome short tandem repeats in Sus scrofa and their variation in European wild boar and domestic pig populations. Anim Genet 2016; 47:682-690. [PMID: 27558303 DOI: 10.1111/age.12483] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 11/27/2022]
Abstract
Y-chromosome markers are important tools for studying male-specific gene flow within and between populations, hybridization patterns and kinship. However, their use in non-human mammals is often hampered by the lack of Y-specific polymorphic markers. We identified new male-specific short tandem repeats (STRs) in Sus scrofa using the available genome sequence. We selected four polymorphic loci (5-10 alleles per locus), falling in one duplicated and two single-copy regions. A total of 32 haplotypes were found by screening 211 individuals from eight wild boar populations across Europe and five domestic pig populations. European wild boar were characterized by significantly higher levels of haplotype diversity compared to European domestic pigs (HD = 0.904 ± 0.011 and HD = 0.491 ± 0.077 respectively). Relationships among STR haplotypes were investigated by combining them with single nucleotide polymorphisms at two linked genes (AMELY and UTY) in a network analysis. A differentiation between wild and domestic populations was observed (FST = 0.229), with commercial breeds sharing no Y haplotype with the sampled wild boar. Similarly, a certain degree of geographic differentiation was observed across Europe, with a number of local private haplotypes and high diversity in northern populations. The described Y-chromosome markers can be useful to track male inheritance and gene flow in wild and domestic populations, promising to provide insights into evolutionary and population genetics in Sus scrofa.
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Affiliation(s)
- L Iacolina
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy. .,Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, Aalborg, 9000, Denmark.
| | - V Brajković
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - A Canu
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - N Šprem
- Department of Fisheries, Beekeeping, Game Management and Special Zoology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - V Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
| | - L Fontanesi
- Division of Animal Science, Department of Agricultural and Food Sciences, University of Bologna, Viale Fanin 46, Bologna, I-40127, Italy
| | - U Saarma
- Department of Zoology, Institute of Ecology and Earth Sciences, University of Tartu, Vanemuise 46, Tartu, 51014, Estonia
| | - M Apollonio
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
| | - M Scandura
- Department of Science for Nature and Environmental Resources, University of Sassari, via Muroni 25, Sassari, I-07100, Italy
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Contact Zone of Asian and European Wild Boar at North West of Iran. PLoS One 2016; 11:e0159499. [PMID: 27442074 PMCID: PMC4956230 DOI: 10.1371/journal.pone.0159499] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 07/04/2016] [Indexed: 11/19/2022] Open
Abstract
Wild boar (Sus scrofa) are widely distributed throughout the Old World. Most studies have focused on Europe and East Asia with the genetic diversity of West Asia being less well studied. In particular, the genetic variability and genetic structure of the Iranian populations are not yet known; gaps which prevent scientists from resolving the genetic relationships of the Eurasian wild boar. This paper is the first attempt to provide information about genetic relationships among modern Iranian populations of the Eurasian wild boar (S. scrofa) by sequencing 572 bp of the mitochondrial (mt) DNA control region. As a result of this investigation, it was discovered that Iran contains not only Middle Eastern haplotypes, but also shares haplotypes with Europe and East Asia. The Italian clade, which is endemic in Italy, is not identified in Iran, while all other clades, including Asiatic, European, Near East 1, and Near East 2 are found based on the phylogenetic tree and median-joining network. The results of this study illustrate that north west of Iran (specifically Southwest Caspian Sea) is the contact zone between the Asian (Near Eastern and Far Eastern), and the European clades. In light of the fact that the domestication of pigs occurs in Anatolia, this finding is important.
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Yamazaki Y, Adachi F, Sawamura A. Multiple Origins and Admixture of Recently Expanding Japanese Wild Boar (Sus scrofa leucomystax) Populations in Toyama Prefecture of Japan. Zoolog Sci 2016; 33:38-43. [PMID: 26853867 DOI: 10.2108/zs150092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Japanese wild boar (Sus scrofa leucomystax) populations have expanded drastically throughout the Japanese Archipelago in recent decades. To elucidate the dispersal patterns of Japanese wild boar in Toyama Prefecture in central Japan, we used a multi-locus microsatellite DNA analysis to determine its population structure and the degree of admixture. The deviation from Hardy-Weinberg equilibrium was detected in either total or separate regional wild boar samples from Toyama Prefecture. This result could be explained by the Wahlund effect resulting from the mixture of samples from different sources. Bayesian structure analysis, assignment test, and factorial correspondence analysis suggested that wild boars around Toyama Prefecture derive from at least two ancestral sources. The migration and possible mating of each individual may have occurred recently and continued in each geographically neighboring region. The present genetic results may be useful for prediction of future dispersal patterns of Japanese wild boar, as well as other animals in expansion.
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Affiliation(s)
- Yuji Yamazaki
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Fuminari Adachi
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Akira Sawamura
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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Conservation priorities of Iberoamerican pig breeds and their ancestors based on microsatellite information. Heredity (Edinb) 2016; 117:14-24. [PMID: 27025169 DOI: 10.1038/hdy.2016.21] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 01/22/2016] [Accepted: 02/02/2016] [Indexed: 01/17/2023] Open
Abstract
Criollo pig breeds are descendants from pigs brought to the American continent starting with Columbus second trip in 1493. Pigs currently play a key role in social economy and community cultural identity in Latin America. The aim of this study was to establish conservation priorities among a comprehensive group of Criollo pig breeds based on a set of 24 microsatellite markers and using different criteria. Spain and Portugal pig breeds, wild boar populations of different European geographic origins and commercial pig breeds were included in the analysis as potential genetic influences in the development of Criollo pig breeds. Different methods, differing in the weight given to within- and between-breed genetic variability, were used in order to estimate the contribution of each breed to global genetic diversity. As expected, the partial contribution to total heterozygosity gave high priority to Criollo pig breeds, whereas Weitzman procedures prioritized Iberian Peninsula breeds. With the combined within- and between-breed approaches, different conservation priorities were achieved. The Core Set methodologies highly prioritized Criollo pig breeds (Cr. Boliviano, Cr. Pacifico, Cr. Cubano and Cr. Guadalupe). However, weighing the between- and within-breed components with FST and 1-FST, respectively, resulted in higher contributions of Iberian breeds. In spite of the different conservation priorities according to the methodology used, other factors in addition to genetic information also need to be considered in conservation programmes, such as the economic, cultural or historical value of the breeds involved.
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Garcia M, Gingras B, Bowling DL, Herbst CT, Boeckle M, Locatelli Y, Fitch WT. Structural Classification of Wild Boar ( Sus scrofa) Vocalizations. Ethology 2016; 122:329-342. [PMID: 27065507 PMCID: PMC4793927 DOI: 10.1111/eth.12472] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Revised: 07/20/2015] [Accepted: 12/28/2015] [Indexed: 11/28/2022]
Abstract
Determining whether a species' vocal communication system is graded or discrete requires definition of its vocal repertoire. In this context, research on domestic pig (Sus scrofa domesticus) vocalizations, for example, has led to significant advances in our understanding of communicative functions. Despite their close relation to domestic pigs, little is known about wild boar (Sus scrofa) vocalizations. The few existing studies, conducted in the 1970s, relied on visual inspections of spectrograms to quantify acoustic parameters and lacked statistical analysis. Here, we use objective signal processing techniques and advanced statistical approaches to classify 616 calls recorded from semi‐free ranging animals. Based on four spectral and temporal acoustic parameters—quartile Q25, duration, spectral flux, and spectral flatness—extracted from a multivariate analysis, we refine and extend the conclusions drawn from previous work and present a statistically validated classification of the wild boar vocal repertoire into four call types: grunts, grunt‐squeals, squeals, and trumpets. While the majority of calls could be sorted into these categories using objective criteria, we also found evidence supporting a graded interpretation of some wild boar vocalizations as acoustically continuous, with the extremes representing discrete call types. The use of objective criteria based on modern techniques and statistics in respect to acoustic continuity advances our understanding of vocal variation. Integrating our findings with recent studies on domestic pig vocal behavior and emotions, we emphasize the importance of grunt‐squeals for acoustic approaches to animal welfare and underline the need of further research investigating the role of domestication on animal vocal communication.
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Affiliation(s)
- Maxime Garcia
- Department of Cognitive Biology University of Vienna Vienna Austria
| | - Bruno Gingras
- Department of Cognitive Biology University of Vienna Vienna Austria
| | - Daniel L Bowling
- Department of Cognitive Biology University of Vienna Vienna Austria
| | - Christian T Herbst
- Voice Research Lab Department of Biophysics Faculty of Science Palacký University Olomouc Czech Republic
| | - Markus Boeckle
- Department of Cognitive Biology University of Vienna Vienna Austria; Department of Psychotherapy and Biopsychosocial Health Danube University Krems Krems Austria
| | - Yann Locatelli
- Réserve de la Haute Touche Muséum National d'Histoire Naturelle Obterre France; Equipe Interactions Cellulaires et Fertilité UMR0085 Physiologie de la Reproduction et des Comportements Institut National de la Recherche Agronomique Nouzilly France
| | - W Tecumseh Fitch
- Department of Cognitive Biology University of Vienna Vienna Austria
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Are the dinaric mountains a boundary between continental and mediterranean wild boar populations in Croatia? EUR J WILDLIFE RES 2016. [DOI: 10.1007/s10344-016-0989-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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49
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Šprem N, Piria M, Prđun S, Novosel H, Treer T. Variation of wild boar reproductive performance in different habitat types: Implications for management. RUSS J ECOL+ 2016. [DOI: 10.1134/s106741361506017x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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50
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DEMİRBAŞ Y, ÖZKAN KOCA A, PAMUKOĞLU N, SERT H, SUCHENTRUNK F. Mitochondrial DNA control region variability of wild boar Sus scrofa with various external phenotypes in Turkey. TURK J ZOOL 2016. [DOI: 10.3906/zoo-1507-45] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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