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Harmoinen J, von Thaden A, Aspi J, Kvist L, Cocchiararo B, Jarausch A, Gazzola A, Sin T, Lohi H, Hytönen MK, Kojola I, Stronen AV, Caniglia R, Mattucci F, Galaverni M, Godinho R, Ruiz-González A, Randi E, Muñoz-Fuentes V, Nowak C. Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples. BMC Genomics 2021; 22:473. [PMID: 34171993 PMCID: PMC8235813 DOI: 10.1186/s12864-021-07761-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/01/2021] [Indexed: 12/25/2022] Open
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07761-5.
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Affiliation(s)
- Jenni Harmoinen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland.
| | - Alina von Thaden
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Biologicum, Frankfurt am Main, Germany
| | - Jouni Aspi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Laura Kvist
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Berardino Cocchiararo
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
| | - Anne Jarausch
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,Institute for Ecology, Evolution and Diversity, Johann Wolfgang Goethe-University, Biologicum, Frankfurt am Main, Germany
| | - Andrea Gazzola
- Association for the Conservation of Biological Diversity, Focşani, Romania
| | - Teodora Sin
- Association for the Conservation of Biological Diversity, Focşani, Romania.,Department of Systems Ecology and Sustainability, Faculty of Biology, University of Bucharest, Bucharest, Romania
| | - Hannes Lohi
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Marjo K Hytönen
- Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland.,Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland.,Folkhälsan Research Center, Helsinki, Finland
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke), Eteläranta 55, FI-96300, Rovaniemi, Finland
| | - Astrid Vik Stronen
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.,Department of Biotechnology and Life Sciences, Insubria University, Varese, Italy
| | - Romolo Caniglia
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research, Bologna, Italy
| | - Federica Mattucci
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research, Bologna, Italy
| | | | - Raquel Godinho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.,Department of Biology, Faculty of Science, University of Porto, Porto, Portugal
| | - Aritz Ruiz-González
- Unit for Conservation Genetics (BIO-CGE), Department for the Monitoring and Protection of the Environment and for Biodiversity Conservation, Italian Institute for Environmental Protection and Research, Bologna, Italy.,Department of Zoology and Animal Cell Biology, Zoology Laboratory, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain
| | - 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
| | - Violeta Muñoz-Fuentes
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Carsten Nowak
- Conservation Genetics Group, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany.,LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt am Main, Germany
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