Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples
Abstract Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is...
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| Format: | Article |
| Language: | English |
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BMC
2021-06-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-021-07761-5 |
| _version_ | 1818848501666152448 |
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| author | Jenni Harmoinen Alina von Thaden Jouni Aspi Laura Kvist Berardino Cocchiararo Anne Jarausch Andrea Gazzola Teodora Sin Hannes Lohi Marjo K. Hytönen Ilpo Kojola Astrid Vik Stronen Romolo Caniglia Federica Mattucci Marco Galaverni Raquel Godinho Aritz Ruiz-González Ettore Randi Violeta Muñoz-Fuentes Carsten Nowak |
| author_facet | Jenni Harmoinen Alina von Thaden Jouni Aspi Laura Kvist Berardino Cocchiararo Anne Jarausch Andrea Gazzola Teodora Sin Hannes Lohi Marjo K. Hytönen Ilpo Kojola Astrid Vik Stronen Romolo Caniglia Federica Mattucci Marco Galaverni Raquel Godinho Aritz Ruiz-González Ettore Randi Violeta Muñoz-Fuentes Carsten Nowak |
| author_sort | Jenni Harmoinen |
| collection | DOAJ |
| description | Abstract Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales. |
| first_indexed | 2024-12-19T06:18:21Z |
| format | Article |
| id | doaj.art-be0ecafd158d467d8444097813b80eb2 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T06:18:21Z |
| publishDate | 2021-06-01 |
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| series | BMC Genomics |
| spelling | doaj.art-be0ecafd158d467d8444097813b80eb22022-12-21T20:32:47ZengBMCBMC Genomics1471-21642021-06-0122111510.1186/s12864-021-07761-5Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samplesJenni Harmoinen0Alina von Thaden1Jouni Aspi2Laura Kvist3Berardino Cocchiararo4Anne Jarausch5Andrea Gazzola6Teodora Sin7Hannes Lohi8Marjo K. Hytönen9Ilpo Kojola10Astrid Vik Stronen11Romolo Caniglia12Federica Mattucci13Marco Galaverni14Raquel Godinho15Aritz Ruiz-González16Ettore Randi17Violeta Muñoz-Fuentes18Carsten Nowak19Ecology and Genetics Research Unit, University of OuluConservation Genetics Group, Senckenberg Research Institute and Natural History Museum FrankfurtEcology and Genetics Research Unit, University of OuluEcology and Genetics Research Unit, University of OuluConservation Genetics Group, Senckenberg Research Institute and Natural History Museum FrankfurtConservation Genetics Group, Senckenberg Research Institute and Natural History Museum FrankfurtAssociation for the Conservation of Biological DiversityAssociation for the Conservation of Biological DiversityDepartment of Veterinary Biosciences, University of HelsinkiDepartment of Veterinary Biosciences, University of HelsinkiNatural Resources Institute Finland (Luke)Department of Biology, Biotechnical Faculty, University of LjubljanaUnit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and ResearchUnit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and ResearchScientific Area, WWF ItalyCIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do PortoUnit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and ResearchDepartment of Biological, Geological and Environmental Sciences, University of BolognaConservation Genetics Group, Senckenberg Research Institute and Natural History Museum FrankfurtConservation Genetics Group, Senckenberg Research Institute and Natural History Museum FrankfurtAbstract Background Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174 K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.https://doi.org/10.1186/s12864-021-07761-5Canis lupusCanis lupus familiarisHybridizationSNP genotypingNon-invasive samplingMuseum samples |
| spellingShingle | Jenni Harmoinen Alina von Thaden Jouni Aspi Laura Kvist Berardino Cocchiararo Anne Jarausch Andrea Gazzola Teodora Sin Hannes Lohi Marjo K. Hytönen Ilpo Kojola Astrid Vik Stronen Romolo Caniglia Federica Mattucci Marco Galaverni Raquel Godinho Aritz Ruiz-González Ettore Randi Violeta Muñoz-Fuentes Carsten Nowak Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples BMC Genomics Canis lupus Canis lupus familiaris Hybridization SNP genotyping Non-invasive sampling Museum samples |
| title | Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples |
| title_full | Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples |
| title_fullStr | Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples |
| title_full_unstemmed | Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples |
| title_short | Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples |
| title_sort | reliable wolf dog hybrid detection in europe using a reduced snp panel developed for non invasively collected samples |
| topic | Canis lupus Canis lupus familiaris Hybridization SNP genotyping Non-invasive sampling Museum samples |
| url | https://doi.org/10.1186/s12864-021-07761-5 |
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