Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations
Present‐day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic intro...
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| Vydáno v: | Molecular ecology Ročník 22; číslo 3; s. 856 - 866 |
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| Hlavní autoři: | , , , , , , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
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Oxford, UK
Blackwell Publishing Ltd
01.02.2013
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| ISSN: | 0962-1083, 1365-294X, 1365-294X |
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| Abstract | Present‐day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far‐reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome‐wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first‐generation hybrids until fifth‐generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced‐generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome‐wide SNP analysis is a promising tool to quantify recent hybridization in free‐living populations. |
|---|---|
| AbstractList | Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations. Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations.Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations. Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified beyond doubt mainly because available methods were unable to quantify the extent of introgression and rule out natural processes. Genetic introgression from domestic pigs may have far-reaching ecological consequences by altering traits like the reproduction rate or immunology of wild boar. In this study, we demonstrate a novel approach to investigate genetic introgression in a Northwest (NW) European wild boar data set using a genome-wide single nucleotide polymorphism (SNP) assay developed for domestic pigs. We quantified the extent of introgression using allele frequency spectrum analysis, in silico hybridization simulations and genome distribution patterns of introgressed SNPs. Levels of recent introgression in the study area were expected to be low, as pig farming practices are prevailingly intensive and indoors. However, evidence was found for geographically widespread presence of domestic pig SNPs in 10% of analysed wild boar. This was supported by the identification of two different pig mitochondrial DNA haplotypes in three of the identified hybrid wild boar, suggesting that introgression had occurred from multiple sources (pig breeds). In silico hybridization simulations showed that the level of introgression in the identified hybrid wild boar is equivalent to first-generation hybrids until fifth-generation backcrosses with wild boar. The distribution pattern of introgressed SNPs supported these assignments in four of nine hybrids. The other five hybrids are considered advanced-generation hybrids, resulting from interbreeding among hybrid individuals. Three of nine hybrids were genetically associated with a different wild boar population than the one in which they were sampled. This discrepancy suggests that genetic introgression has occurred through the escape or release of an already hybridized farmed wild boar stock. We conclude that genetic introgression from domestic pigs into NW European wild boar populations is more recent and more common than expected and that genome-wide SNP analysis is a promising tool to quantify recent hybridization in free-living populations. [PUBLICATION ABSTRACT] |
| Author | LUTZ, W. CROOIJMANS, R. P. M. A. GOEDBLOED, D. J. MEGENS, H.J. YDENBERG, R. C. Van WIEREN, S. E. GROENEN, M. PRINS, H. H. T. Van HOOFT, P. ALEXANDRI, P. HERRERO-MEDRANO, J. M. |
| Author_xml | – sequence: 1 givenname: D. J. surname: GOEDBLOED fullname: GOEDBLOED, D. J. organization: Resource Ecology Group, Wageningen UR, P.O. Box 47, 6700AA Wageningen, The Netherlands – sequence: 2 givenname: H.J. surname: MEGENS fullname: MEGENS, H.J. organization: Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700AH Wageningen, The Netherlands – sequence: 3 givenname: P. surname: Van HOOFT fullname: Van HOOFT, P. organization: Resource Ecology Group, Wageningen UR, P.O. Box 47, 6700AA Wageningen, The Netherlands – sequence: 4 givenname: J. M. surname: HERRERO-MEDRANO fullname: HERRERO-MEDRANO, J. M. organization: Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700AH Wageningen, The Netherlands – sequence: 5 givenname: W. surname: LUTZ fullname: LUTZ, W. organization: Wildlife Research Institute, Pützchens Chaussee 228, 53229 Bonn, Germany – sequence: 6 givenname: P. surname: ALEXANDRI fullname: ALEXANDRI, P. organization: School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece – sequence: 7 givenname: R. P. M. A. surname: CROOIJMANS fullname: CROOIJMANS, R. P. M. A. organization: Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700AH Wageningen, The Netherlands – sequence: 8 givenname: M. surname: GROENEN fullname: GROENEN, M. organization: Animal Breeding and Genomics Centre, Wageningen UR, P.O. Box 338, 6700AH Wageningen, The Netherlands – sequence: 9 givenname: S. E. surname: Van WIEREN fullname: Van WIEREN, S. E. organization: Resource Ecology Group, Wageningen UR, P.O. Box 47, 6700AA Wageningen, The Netherlands – sequence: 10 givenname: R. C. surname: YDENBERG fullname: YDENBERG, R. C. organization: Resource Ecology Group, Wageningen UR, P.O. Box 47, 6700AA Wageningen, The Netherlands – sequence: 11 givenname: H. H. T. surname: PRINS fullname: PRINS, H. H. T. organization: Resource Ecology Group, Wageningen UR, P.O. Box 47, 6700AA Wageningen, The Netherlands |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/22731769$$D View this record in MEDLINE/PubMed |
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| References | Verhoeven KJ, Macel M, Wolfe LM, Biere A (2011) Population admixture, biological invasions and the balance between local adaptation and inbreeding depression. Proceedings of the Royal Society B-Biological Sciences, 278, 2-8. Giuffra E, Kijas JMH, Amarger V et al. (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics, 154, 1785-1791. Miller JM, Poissant J, Kijas JW, Coltman DW (2011) A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Molecular Ecology Resources, 11, 314-322. Seeb JE, Carvalho G, Hauser L et al. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology Resources, 11(Suppl 1), 1-8. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular Biology and Evolution, 24, 1596-1599. 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those of European domestic pigs with 2n=38 publication-title: Animal Genetics – volume: 101 start-page: 797 year: 2010 end-page: 822 article-title: Genetic diversity of wild boar populations and domestic pig breeds ( ) in South‐western Europe publication-title: Biological Journal of the Linnean Society – volume: 19 start-page: 208 year: 2004 end-page: 216 article-title: SNPs in ecology, evolution and conservation publication-title: Trends in Ecology & Evolution – volume: 54 start-page: 680 year: 2010 end-page: 686 article-title: Multiple Asian pig origins revealed through genomic analyses publication-title: Molecular Phylogenetics and Evolution – year: 1990 – volume: 2 start-page: e190 year: 2006 article-title: Population structure and eigenanalysis publication-title: PLoS Genetics – volume: 267 start-page: 89 year: 2005 end-page: 96 article-title: The influence of food and temperature on population density of wild boar in the Thurgau (Switzerland) publication-title: Journal of Zoology 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fine geographical scales with microsatellites and single nucleotide polymorphisms publication-title: Molecular Ecology – volume: 41 start-page: 125 year: 2011 end-page: 137 article-title: Genetic diversity in the European wild boar : phylogeography, population structure and wild × domestic hybridization publication-title: Mammal Review – volume: 19 start-page: 968 year: 2010 end-page: 984 article-title: Genome‐wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies publication-title: Molecular Ecology – volume: 53 start-page: 287 year: 2007 end-page: 297 article-title: Reproductive parameters of wild boar ( ) in three different parts of Germany publication-title: European Journal of Wildlife Research – volume: 4 start-page: e6524 year: 2009 article-title: Design of a high‐density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology publication-title: PLoS ONE – volume: 11 start-page: 1 issue: Suppl 1 year: 2011 end-page: 8 article-title: Single‐nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms publication-title: Molecular Ecology Resources – volume: 24 start-page: 1596 year: 2007 end-page: 1599 article-title: MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0 publication-title: Molecular Biology and Evolution – volume: 278 start-page: 2 year: 2011 end-page: 8 article-title: Population admixture, biological invasions and the balance between local adaptation and inbreeding depression publication-title: Proceedings of the Royal Society B-Biological Sciences – volume: 23 start-page: 4992 year: 1995 end-page: 4999 article-title: A new DNA sequence assembly program publication-title: Nucleic Acids Research – volume: 12 start-page: article no. 150 year: 2011 article-title: Genome wide SNP discovery, analysis and evaluation in mallard ( ) publication-title: BMC Genomics – volume: 16 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| Snippet | Present‐day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified... Present-day genetic introgression from domestic pigs into European wild boar has been suggested in various studies. However, no hybrids have been identified... |
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| SubjectTerms | Agricultural practices Animal populations Animals Distribution patterns DNA, Mitochondrial - genetics Domestic animals domestic pig Ecological effects Europe Genetics Genetics, Population Genomes Haplotypes Heterozygote Hogs Hybridization Hybridization, Genetic Hybrids Immunology introgression Mitochondrial DNA Molecular Sequence Data Polymorphism Polymorphism, Single Nucleotide Sequence Analysis, DNA single nucleotide polymorphism Sus scrofa Sus scrofa - genetics Swine wild boar Wildlife |
| Title | Genome-wide single nucleotide polymorphism analysis reveals recent genetic introgression from domestic pigs into Northwest European wild boar populations |
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