Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples
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....
Published in: | BMC Genomics |
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Main Authors: | , , , , , , , , , , , , , , , , , , , |
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Language: | English |
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BMC
2021
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Online Access: | http://hdl.handle.net/10138/332787 |
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/332787 |
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Open Polar |
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HELDA – University of Helsinki Open Repository |
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ftunivhelsihelda |
language |
English |
topic |
Canis lupus Canis lupus familiaris Hybridization SNP genotyping Non-invasive sampling Museum samples POPULATION-STRUCTURE CANIS-LUPUS DOMESTIC DOGS GENETIC DIVERSITY WOLVES ADMIXTURE PATTERNS MARKERS SIZE 413 Veterinary science 1184 Genetics developmental biology physiology |
spellingShingle |
Canis lupus Canis lupus familiaris Hybridization SNP genotyping Non-invasive sampling Museum samples POPULATION-STRUCTURE CANIS-LUPUS DOMESTIC DOGS GENETIC DIVERSITY WOLVES ADMIXTURE PATTERNS MARKERS SIZE 413 Veterinary science 1184 Genetics developmental biology physiology Harmoinen, Jenni von Thaden, Alina Aspi, Jouni Kvist, Laura Cocchiararo, Berardino Jarausch, Anne Gazzola, Andrea Sin, Teodora Lohi, Hannes Hytönen, Marjo K. Kojola, Ilpo Stronen, Astrid Vik Caniglia, Romolo Mattucci, Federica Galaverni, Marco Godinho, Raquel Ruiz-Gonzalez, Aritz Randi, Ettore Munoz-Fuentes, Violeta Nowak, Carsten Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples |
topic_facet |
Canis lupus Canis lupus familiaris Hybridization SNP genotyping Non-invasive sampling Museum samples POPULATION-STRUCTURE CANIS-LUPUS DOMESTIC DOGS GENETIC DIVERSITY WOLVES ADMIXTURE PATTERNS MARKERS SIZE 413 Veterinary science 1184 Genetics developmental biology physiology |
description |
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. Peer reviewed |
author2 |
Helsinki One Health (HOH) Hannes Tapani Lohi / Principal Investigator Veterinary Genetics Veterinary Biosciences Biosciences Department of Medical and Clinical Genetics Medicum |
format |
Article in Journal/Newspaper |
author |
Harmoinen, Jenni von Thaden, Alina Aspi, Jouni Kvist, Laura Cocchiararo, Berardino Jarausch, Anne Gazzola, Andrea Sin, Teodora Lohi, Hannes Hytönen, Marjo K. Kojola, Ilpo Stronen, Astrid Vik Caniglia, Romolo Mattucci, Federica Galaverni, Marco Godinho, Raquel Ruiz-Gonzalez, Aritz Randi, Ettore Munoz-Fuentes, Violeta Nowak, Carsten |
author_facet |
Harmoinen, Jenni von Thaden, Alina Aspi, Jouni Kvist, Laura Cocchiararo, Berardino Jarausch, Anne Gazzola, Andrea Sin, Teodora Lohi, Hannes Hytönen, Marjo K. Kojola, Ilpo Stronen, Astrid Vik Caniglia, Romolo Mattucci, Federica Galaverni, Marco Godinho, Raquel Ruiz-Gonzalez, Aritz Randi, Ettore Munoz-Fuentes, Violeta Nowak, Carsten |
author_sort |
Harmoinen, Jenni |
title |
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_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_sort |
reliable wolf-dog hybrid detection in europe using a reduced snp panel developed for non-invasively collected samples |
publisher |
BMC |
publishDate |
2021 |
url |
http://hdl.handle.net/10138/332787 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_relation |
10.1186/s12864-021-07761-5 JH received funding from the Maj and Tor Nessling Foundation, the Finnish Cultural Foundation and Emil Aaltonen Foundation. Laboratory analyses were cofounded by the (LOEWE) program (Landes-Offensive zur Entwicklung Wissenschaftlich-okonomischer Exzellenz) of the German Federal State of Hessen. AvT received funding from the Karl und Marie Schack-Stiftung. RG was supported by the Portuguese Foundation for Science and Technology (FCT, DL57/2016). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Harmoinen , J , von Thaden , A , Aspi , J , Kvist , L , Cocchiararo , B , Jarausch , A , Gazzola , A , Sin , T , Lohi , H , Hytönen , M K , Kojola , I , Stronen , A V , Caniglia , R , Mattucci , F , Galaverni , M , Godinho , R , Ruiz-Gonzalez , A , Randi , E , Munoz-Fuentes , V & Nowak , C 2021 , ' Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples ' , BMC Genomics , vol. 22 , no. 1 , 473 . https://doi.org/10.1186/s12864-021-07761-5 ORCID: /0000-0003-1976-5874/work/98019642 49ba4d26-7c3c-408f-9368-e107fbbe7e71 http://hdl.handle.net/10138/332787 000669606700001 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
container_title |
BMC Genomics |
container_volume |
22 |
container_issue |
1 |
_version_ |
1787423575863459840 |
spelling |
ftunivhelsihelda:oai:helda.helsinki.fi:10138/332787 2024-01-07T09:42:34+01:00 Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples Harmoinen, Jenni von Thaden, Alina Aspi, Jouni Kvist, Laura Cocchiararo, Berardino Jarausch, Anne Gazzola, Andrea Sin, Teodora Lohi, Hannes Hytönen, Marjo K. Kojola, Ilpo Stronen, Astrid Vik Caniglia, Romolo Mattucci, Federica Galaverni, Marco Godinho, Raquel Ruiz-Gonzalez, Aritz Randi, Ettore Munoz-Fuentes, Violeta Nowak, Carsten Helsinki One Health (HOH) Hannes Tapani Lohi / Principal Investigator Veterinary Genetics Veterinary Biosciences Biosciences Department of Medical and Clinical Genetics Medicum 2021-08-03T10:10:01Z 15 application/pdf http://hdl.handle.net/10138/332787 eng eng BMC 10.1186/s12864-021-07761-5 JH received funding from the Maj and Tor Nessling Foundation, the Finnish Cultural Foundation and Emil Aaltonen Foundation. Laboratory analyses were cofounded by the (LOEWE) program (Landes-Offensive zur Entwicklung Wissenschaftlich-okonomischer Exzellenz) of the German Federal State of Hessen. AvT received funding from the Karl und Marie Schack-Stiftung. RG was supported by the Portuguese Foundation for Science and Technology (FCT, DL57/2016). The funding bodies played no role in the design of the study and collection, analysis, and interpretation of data and in writing the manuscript. Harmoinen , J , von Thaden , A , Aspi , J , Kvist , L , Cocchiararo , B , Jarausch , A , Gazzola , A , Sin , T , Lohi , H , Hytönen , M K , Kojola , I , Stronen , A V , Caniglia , R , Mattucci , F , Galaverni , M , Godinho , R , Ruiz-Gonzalez , A , Randi , E , Munoz-Fuentes , V & Nowak , C 2021 , ' Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples ' , BMC Genomics , vol. 22 , no. 1 , 473 . https://doi.org/10.1186/s12864-021-07761-5 ORCID: /0000-0003-1976-5874/work/98019642 49ba4d26-7c3c-408f-9368-e107fbbe7e71 http://hdl.handle.net/10138/332787 000669606700001 cc_by openAccess info:eu-repo/semantics/openAccess Canis lupus Canis lupus familiaris Hybridization SNP genotyping Non-invasive sampling Museum samples POPULATION-STRUCTURE CANIS-LUPUS DOMESTIC DOGS GENETIC DIVERSITY WOLVES ADMIXTURE PATTERNS MARKERS SIZE 413 Veterinary science 1184 Genetics developmental biology physiology Article publishedVersion 2021 ftunivhelsihelda 2023-12-14T00:12:25Z 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. Peer reviewed Article in Journal/Newspaper Canis lupus HELDA – University of Helsinki Open Repository BMC Genomics 22 1 |