Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)
Abstract The rapid expansion of wild pigs (Sus scrofa) throughout the United States has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2024-02-01
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| Series: | Ecosphere |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/ecs2.4774 |
| _version_ | 1827312499340345344 |
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| author | Timothy J. Smyser Peter Pfaffelhuber Rachael M. Giglio Matthew G. DeSaix Amy J. Davis Courtney F. Bowden Michael A. Tabak Arianna Manunza Valentin Adrian Bâlteanu Marcel Amills Laura Iacolina Pamela Walker Carl Lessard Antoinette J. Piaggio |
| author_facet | Timothy J. Smyser Peter Pfaffelhuber Rachael M. Giglio Matthew G. DeSaix Amy J. Davis Courtney F. Bowden Michael A. Tabak Arianna Manunza Valentin Adrian Bâlteanu Marcel Amills Laura Iacolina Pamela Walker Carl Lessard Antoinette J. Piaggio |
| author_sort | Timothy J. Smyser |
| collection | DOAJ |
| description | Abstract The rapid expansion of wild pigs (Sus scrofa) throughout the United States has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs—which overwhelmingly represent domestic pig and wild boar hybrids—pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pig found within the United States. We organized reference high‐density single nucleotide polymorphism genotypes (1039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed‐commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well‐established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern. |
| first_indexed | 2024-03-07T19:46:05Z |
| format | Article |
| id | doaj.art-18a946b90e734dab9218d5d3c5b7be65 |
| institution | Directory Open Access Journal |
| issn | 2150-8925 |
| language | English |
| last_indexed | 2024-04-24T21:44:22Z |
| publishDate | 2024-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Ecosphere |
| spelling | doaj.art-18a946b90e734dab9218d5d3c5b7be652024-03-21T02:06:54ZengWileyEcosphere2150-89252024-02-01152n/an/a10.1002/ecs2.4774Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa)Timothy J. Smyser0Peter Pfaffelhuber1Rachael M. Giglio2Matthew G. DeSaix3Amy J. Davis4Courtney F. Bowden5Michael A. Tabak6Arianna Manunza7Valentin Adrian Bâlteanu8Marcel Amills9Laura Iacolina10Pamela Walker11Carl Lessard12Antoinette J. Piaggio13United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center Fort Collins Colorado USADepartment of Mathematical Stochastics University of Freiburg Freiburg im Breisgau Baden‐Württemberg GermanyUnited States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center Fort Collins Colorado USAUnited States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center Fort Collins Colorado USAUnited States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center Fort Collins Colorado USAUnited States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center Fort Collins Colorado USAQuantitative Science Consulting, LLC Melancthon Ontario CanadaNational Research Council Institute of Agricultural Biology and Biotechnology Milan ItalyLaboratory of Genomics, Animal Breeding, Biodiversity and Molecular Pathology University of Agricultural Sciences and Veterinary Medicine Cluj‐Napoca Cluj‐Napoca RomaniaCentre for Research in Agricultural Genomics (CRAG), CSIC‐IRTA‐UAB‐UB, Universitat Autònoma de Barcelona Bellaterra Catalonia SpainFaculty of Mathematics, Natural Sciences and Information Technologies University of Primorska Koper SloveniaAnimal Genetic Resources of Canada, Agriculture and Agri‐Food Canada Saskatoon Saskatchewan CanadaAnimal Genetic Resources of Canada, Agriculture and Agri‐Food Canada Saskatoon Saskatchewan CanadaUnited States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center Fort Collins Colorado USAAbstract The rapid expansion of wild pigs (Sus scrofa) throughout the United States has been fueled by unlawful introductions, with invasive populations causing extensive crop losses, damaging native ecosystems, and serving as a reservoir for disease. Multiple states have passed laws prohibiting the possession or transport of wild pigs. However, genetic and phenotypic similarities between domestic pigs and invasive wild pigs—which overwhelmingly represent domestic pig and wild boar hybrids—pose a challenge for the enforcement of such regulations. We sought to exploit wild boar ancestry as a common attribute among the vast majority of invasive wild pigs as a means of genetically differentiating wild pigs from breeds of domestic pig found within the United States. We organized reference high‐density single nucleotide polymorphism genotypes (1039 samples from 33 domestic breeds and 382 samples from 16 wild boar populations) into five genetically cohesive reference groups: mixed‐commercial breeds, Durocs, heritage breeds, primitive breeds, and wild boar. Building upon well‐established genetic clustering approaches, we structured the test statistic to describe the difference in the likelihood of a given genotype's ancestry vectors (sensu genetic clustering analysis) if derived strictly from the four described domestic pig reference groups versus allowing for admixture from the wild boar group. By fitting statistical distributions to test statistics of reference domestic pigs, we characterized the distribution of the null hypothesis that a given genotype descends strictly from domestic pig reference groups. We tested the approach with simulated genotypes and empirical data from an additional 29 breeds of domestic pig represented by 435 unique genotypes; all associated test statistics for simulated and empirical domestic pig challenge sets fell within the distribution of reference domestic pigs. We then evaluated 6566 invasive wild pigs sampled across the contiguous United States, of which 63% exceeded the maximum threshold for domestic pigs and could be statistically classified as possessing wild boar ancestry. This approach provides a scientific foundation to enforce regulations prohibiting the possession of this destructive invasive species. Further, this computationally efficient and generalizable approach could be readily adapted to quantify gene flow among ecological systems of conservation or management concern.https://doi.org/10.1002/ecs2.4774ancestryexoferalizationferal swinegenetic clusteringgenetic identificationhybridization |
| spellingShingle | Timothy J. Smyser Peter Pfaffelhuber Rachael M. Giglio Matthew G. DeSaix Amy J. Davis Courtney F. Bowden Michael A. Tabak Arianna Manunza Valentin Adrian Bâlteanu Marcel Amills Laura Iacolina Pamela Walker Carl Lessard Antoinette J. Piaggio Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa) Ecosphere ancestry exoferalization feral swine genetic clustering genetic identification hybridization |
| title | Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa) |
| title_full | Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa) |
| title_fullStr | Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa) |
| title_full_unstemmed | Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa) |
| title_short | Probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs (Sus scrofa) |
| title_sort | probabilistic genetic identification of wild boar hybridization to support control of invasive wild pigs sus scrofa |
| topic | ancestry exoferalization feral swine genetic clustering genetic identification hybridization |
| url | https://doi.org/10.1002/ecs2.4774 |
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