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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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Ryan J, Prentis PJ, Fuller S. Multiscale landscape genetic analysis identifies major waterways as a barrier to dispersal of feral pigs in north Queensland, Australia. Ecol Evol 2023; 13:e10575. [PMID: 37780088 PMCID: PMC10539047 DOI: 10.1002/ece3.10575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023] Open
Abstract
Feral pigs (Sus scrofa) are a destructive and widespread invasive pest in Australia. An understanding of feral pig movement is required to develop management strategies to control feral pigs in Australia. Because landscape structure can have a strong influence on animal movement, it is important to determine how landscape features facilitate or impede the movement of feral pigs. Consequently, we conducted a landscape genetic analysis of feral pig populations in the Herbert region of far north Queensland, Australia, to determine management units and provide recommendations to better inform feral pig population control strategies. Using microsatellite data obtained from 256 feral pig samples from 44 sites, we examined feral pig population structure at multiple spatial scales for univariate and multivariate landscape resistance surfaces to determine the optimal spatial scale and to identify which of the nine landscape features tested impede or facilitate feral pig gene flow. Only weak genetic structure was found among the 44 sampling sites, but major waterways were identified as a minor barrier to gene flow, and an isolation by distance model was supported. We also found that highways facilitated gene flow across the study area, and this suggests that they may act as movement corridors or indicate translocation of feral pigs. Additionally, incorporating a second spatial scale enhanced the ability of our landscape genetics analysis to detect the influence of landscape structure on gene flow. We identified three management units based on natural barriers to gene flow and future targeted control should be undertaken in these management units to deliver sustained reduction of feral pig populations in the Herbert region. This study demonstrates how a landscape genetic approach can be used to gain insight into the ecology of an invasive pest species and be used to develop population control strategies which utilise natural barriers to movement.
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Affiliation(s)
- James Ryan
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Peter J. Prentis
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
- Centre for Agriculture and the BioeconomyQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Susan Fuller
- School of Biology and Environmental ScienceQueensland University of TechnologyBrisbaneQueenslandAustralia
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3
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Introduced, Mixed, and Peripheral: Conservation of Mitochondrial-DNA Lineages in the Wild Boar (Sus scrofa L.) Population in the Urals. DIVERSITY 2022. [DOI: 10.3390/d14110916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Translocations and introductions are important events that allow organisms to overcome natural barriers. The genetic background of colonization success and genetic consequences of the establishment of populations in new environments are of great interest for predicting species’ colonization success. The wild boar has been introduced into many parts of the world. We analyzed sequences of the mitochondrial-DNA control region in the wild boars introduced into the Ural region and compared them with sequences from founder populations (from Europe, the Caucasus, Central Asia, and the Far East). We found that the introduced population has high genetic diversity. Haplotypes from all the major phylogenetic clades were detected in the analyzed group of the animals from the Urals. In this group, no haplotypes identical to Far Eastern sequences were detectable despite a large number of founders from that region. The contribution of lineages originating from Eastern Europe was greater than expected from the proportions (%) of European and Asian animals in the founder populations. This is the first study on the genetic diversity and structure of a wild boar population of mixed origin at the northern periphery of this species’ geographical range.
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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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5
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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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6
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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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7
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Assessing Sus scrofa diversity among continental United States, and Pacific islands populations using molecular markers from a gene banks collection. Sci Rep 2019; 9:3173. [PMID: 30816173 PMCID: PMC6395668 DOI: 10.1038/s41598-019-39309-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 01/07/2019] [Indexed: 11/11/2022] Open
Abstract
Human migration and trade facilitated domesticated livestock movement, gene flow and development of diverse populations upon which agriculture is based. In addition, varying USA ecological conditions has led to a diverse set of livestock populations to utilize. Quantifying genetic diversity of these populations is incomplete. This paper quantifies genetic diversity captured by the National Animal Germplasm Program and explores genetic structure and differences among 19 pig populations (feral populations from Pacific islands, continental US, and Chinese breeds) using 70,231 SNP from 500 animal samples. Among continental US breeds Fis was consistently low suggesting genetic variability is sufficiently available for breeders to use. A unique population structure using principal component analysis illustrated clear distinctions between Duroc, Yorkshire, Hampshire, breeds of Chinese origin, and feral Pacific Island populations were identified. Five Y chromosome haplotypes were evaluated and demonstrated migration patterns from European, central Asia, and potentially Polynesian waves of gene flow. Quantifying diversity and potential origin of Pacific populations provides insight for future uses, and the need for preservation. Viewing gene bank holdings in context of diversity measures we found a lack of inbreeding within breeds, suggesting the collection represents a wide sampling of individual breeds.
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8
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McCann BE, Smyser TJ, Schmit BS, Newman RA, Piaggio AJ, Malek MJ, Swafford SR, Sweitzer RA, Simmons RB. Molecular population structure for feral swine in the United States. J Wildl Manage 2018. [DOI: 10.1002/jwmg.21452] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Blake E. McCann
- Resource Management, Wildlife, Theodore Roosevelt National Park315 2nd Avenue, P.O. Box 7MedoraND 58645USA
| | - Timothy J. Smyser
- U.S. Department of Agriculture, Wildlife Services4101 La Porte AvenueFort CollinsCO 80521USA
| | - Brandon S. Schmit
- U.S. Department of Agriculture, Wildlife Services4101 La Porte AvenueFort CollinsCO 80521USA
| | - Robert A. Newman
- Department of BiologyUniversity of North Dakota10 Cornell Street, Stop 9019Grand ForksND 58202USA
| | - Antoinette J. Piaggio
- U.S. Department of Agriculture, Wildlife Services4101 La Porte AvenueFort CollinsCO 80521USA
| | - Mathew J. Malek
- University of South DakotaSanford School of MedicineDepartment of General Surgery1400 West 22nd StreetSioux FallsSD 57105USA
| | - Seth R. Swafford
- U.S. Fish and Wildlife Service12595 MS Highway 149Yazoo CityMS 39194USA
| | | | - Rebecca B. Simmons
- Department of BiologyUniversity of North Dakota10 Cornell Street, Stop 9019Grand ForksND 58202USA
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9
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Williams KE, Huyvaert KP, Vercauteren KC, Davis AJ, Piaggio AJ. Detection and persistence of environmental DNA from an invasive, terrestrial mammal. Ecol Evol 2017; 8:688-695. [PMID: 29321905 PMCID: PMC5756866 DOI: 10.1002/ece3.3698] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/06/2017] [Accepted: 11/10/2017] [Indexed: 11/10/2022] Open
Abstract
Invasive Sus scrofa, a species commonly referred to as wild pig or feral swine, is a destructive invasive species with a rapidly expanding distribution across the United States. We used artificial wallows and small waterers to determine the minimum amount of time needed for pig eDNA to accumulate in the water source to a detectable level. We removed water from the artificial wallows and tested eDNA detection over the course of 2 weeks to understand eDNA persistence. We show that our method is sensitive enough to detect very low quantities of eDNA shed by a terrestrial mammal that has limited interaction with water. Our experiments suggest that the number of individuals shedding into a water system can affect persistence of eDNA. Use of an eDNA detection technique can benefit management efforts by providing a sensitive method for finding even small numbers of individuals that may be elusive using other methods.
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Affiliation(s)
- Kelly E Williams
- Wildlife Genetics Lab USDA, Wildlife Services, National Wildlife Research Center Fort Collins CO USA.,Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins CO USA.,School of Environmental and Forest Sciences University of Washington Seattle WA USA
| | - Kathryn P Huyvaert
- Department of Fish, Wildlife, and Conservation Biology Colorado State University Fort Collins CO USA
| | - Kurt C Vercauteren
- Wildlife Genetics Lab USDA, Wildlife Services, National Wildlife Research Center Fort Collins CO USA
| | - Amy J Davis
- Wildlife Genetics Lab USDA, Wildlife Services, National Wildlife Research Center Fort Collins CO USA
| | - Antoinette J Piaggio
- Wildlife Genetics Lab USDA, Wildlife Services, National Wildlife Research Center Fort Collins CO USA
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10
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Robeson MS, Khanipov K, Golovko G, Wisely SM, White MD, Bodenchuck M, Smyser TJ, Fofanov Y, Fierer N, Piaggio AJ. Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig ( Sus scrofa). Ecol Evol 2017; 8:185-196. [PMID: 29321862 PMCID: PMC5756863 DOI: 10.1002/ece3.3638] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/11/2017] [Accepted: 10/20/2017] [Indexed: 01/20/2023] Open
Abstract
Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free‐ranging exotic ungulate in the United States. Large and ever‐increasing populations of wild pigs negatively impact agriculture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 billion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing‐based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated blocking primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of blocking primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is significantly different between the three areas sampled, demonstrating this approach is suitable for describing differences in diet composition among the locations.
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Affiliation(s)
- Michael S Robeson
- Fish and Wildlife Conservation Biology Colorado State University Fort Collins CO USA.,USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA.,Present address: Department of Biomedical Informatics College of Medicine University of Arkansas for Medical Sciences Little Rock AR USA
| | - Kamil Khanipov
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - George Golovko
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - Samantha M Wisely
- Department of Wildlife Ecology and Conservation USA 5 USDA, Wildlife Services University of Florida Gainesville FL USA
| | | | | | - Timothy J Smyser
- USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA
| | - Yuriy Fofanov
- Department of Pharmacology The University of Texas Medical Branch Galveston TX USA
| | - Noah Fierer
- Department of Ecology and Evolutionary Biology Cooperative Institute for Research in Environmental Sciences University of Colorado Boulder CO USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services National Wildlife Research Center Wildlife Genetics Lab Fort Collins CO USA
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11
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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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12
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Osei-Amponsah R, Skinner BM, Adjei DO, Bauer J, Larson G, Affara NA, Sargent CA. Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis. BMC Genomics 2017; 18:193. [PMID: 28219344 PMCID: PMC5319064 DOI: 10.1186/s12864-017-3536-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/02/2017] [Indexed: 12/12/2022] Open
Abstract
Background The Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping. Results The study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits. Conclusions The presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3536-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Osei-Amponsah
- Animal Breeding and Genetics Research Group, Department of Animal Science, University of Ghana, P. O. Box LG 226, Legon-ACCRA, Ghana.,Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Benjamin M Skinner
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Dennis O Adjei
- Animal Breeding and Genetics Research Group, Department of Animal Science, University of Ghana, P. O. Box LG 226, Legon-ACCRA, Ghana
| | - Julien Bauer
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford, OX1 3QY, UK
| | - Nabeel A Affara
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK
| | - Carole A Sargent
- Mammalian Genetics Research Group, Department of Pathology, University of Cambridge, Tennis Court Rd, Cambridge, CB2 1QP, UK.
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13
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Snow NP, Jarzyna MA, VerCauteren KC. Interpreting and predicting the spread of invasive wild pigs. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.12866] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nathan P. Snow
- Caesar Kleberg Wildlife Research Institute Texas A&M University‐Kingsville Kingsville TX 78363 USA
| | - Marta A. Jarzyna
- Department of Ecology and Evolutionary Biology Yale University New Haven CT 06520 USA
| | - Kurt C. VerCauteren
- USDA/APHIS/Wildlife Services National Wildlife Research Center Fort Collins CO 80521 USA
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14
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McClure ML, Burdett CL, Farnsworth ML, Lutman MW, Theobald DM, Riggs PD, Grear DA, Miller RS. Modeling and mapping the probability of occurrence of invasive wild pigs across the contiguous United States. PLoS One 2015; 10:e0133771. [PMID: 26267266 PMCID: PMC4534449 DOI: 10.1371/journal.pone.0133771] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 07/01/2015] [Indexed: 11/19/2022] Open
Abstract
Wild pigs (Sus scrofa), also known as wild swine, feral pigs, or feral hogs, are one of the most widespread and successful invasive species around the world. Wild pigs have been linked to extensive and costly agricultural damage and present a serious threat to plant and animal communities due to their rooting behavior and omnivorous diet. We modeled the current distribution of wild pigs in the United States to better understand the physiological and ecological factors that may determine their invasive potential and to guide future study and eradication efforts. Using national-scale wild pig occurrence data reported between 1982 and 2012 by wildlife management professionals, we estimated the probability of wild pig occurrence across the United States using a logistic discrimination function and environmental covariates hypothesized to influence the distribution of the species. Our results suggest the distribution of wild pigs in the U.S. was most strongly limited by cold temperatures and availability of water, and that they were most likely to occur where potential home ranges had higher habitat heterogeneity, providing access to multiple key resources including water, forage, and cover. High probability of occurrence was also associated with frequent high temperatures, up to a high threshold. However, this pattern is driven by pigs’ historic distribution in warm climates of the southern U.S. Further study of pigs’ ability to persist in cold northern climates is needed to better understand whether low temperatures actually limit their distribution. Our model highlights areas at risk of invasion as those with habitat conditions similar to those found in pigs’ current range that are also near current populations. This study provides a macro-scale approach to generalist species distribution modeling that is applicable to other generalist and invasive species.
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Affiliation(s)
- Meredith L. McClure
- Conservation Science Partners, Truckee, California, United States of America
- * E-mail: (MLM); (RSM)
| | - Christopher L. Burdett
- Department of Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | - Mark W. Lutman
- National Wildlife Disease Program, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, United States of America
| | - David M. Theobald
- Conservation Science Partners, Truckee, California, United States of America
| | - Philip D. Riggs
- Center for Epidemiology and Animal Health, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, United States of America
| | - Daniel A. Grear
- Center for Epidemiology and Animal Health, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, United States of America
| | - Ryan S. Miller
- Center for Epidemiology and Animal Health, Animal and Plant Health Inspection Service, United States Department of Agriculture, Fort Collins, Colorado, United States of America
- * E-mail: (MLM); (RSM)
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