Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples
For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide po...
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Uppsala universitet, Evolutionsbiologi
2021
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ftuppsalauniv:oai:DiVA.org:uu-468631 2024-02-11T10:04:31+01:00 Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples Ekblom, Robert Aronsson, Malin Elsner-Gearing, Franziska Johansson, Malin Fountain, Toby Persson, Jens 2021 application/pdf http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-468631 https://doi.org/10.1007/s12686-021-01208-5 eng eng Uppsala universitet, Evolutionsbiologi Uppsala universitet, Institutionen för ekologi och genetik Swedish Environm Protect Agcy, S-10648 Stockholm, Sweden Swedish Univ Agr Sci, Dept Ecol, Grimso Wildlife Res Stn, S-73091 Riddarhyttan, Sweden. Springer Nature Conservation Genetics Resources, 1877-7252, 2021, 13:3, s. 261-274 orcid:0000-0003-2222-1966 orcid:0000-0002-5501-4691 orcid:0000-0003-1405-7561 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-468631 doi:10.1007/s12686-021-01208-5 ISI:000642384800001 info:eu-repo/semantics/openAccess Wolverine Conservation Single nucleotide polymorphisms Population genetics Relatedness Pedigree Genetics Genetik Article in journal info:eu-repo/semantics/article text 2021 ftuppsalauniv https://doi.org/10.1007/s12686-021-01208-5 2024-01-17T23:32:44Z For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey. Article in Journal/Newspaper Gulo gulo Uppsala University: Publications (DiVA) Conservation Genetics Resources 13 3 261 274 |
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Open Polar |
collection |
Uppsala University: Publications (DiVA) |
op_collection_id |
ftuppsalauniv |
language |
English |
topic |
Wolverine Conservation Single nucleotide polymorphisms Population genetics Relatedness Pedigree Genetics Genetik |
spellingShingle |
Wolverine Conservation Single nucleotide polymorphisms Population genetics Relatedness Pedigree Genetics Genetik Ekblom, Robert Aronsson, Malin Elsner-Gearing, Franziska Johansson, Malin Fountain, Toby Persson, Jens Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples |
topic_facet |
Wolverine Conservation Single nucleotide polymorphisms Population genetics Relatedness Pedigree Genetics Genetik |
description |
For conservation genetic studies using non-invasively collected samples, genome-wide data may be hard to acquire. Until now, such studies have instead mostly relied on analyses of traditional genetic markers such as microsatellites (SSRs). Recently, high throughput genotyping of single nucleotide polymorphisms (SNPs) has become available, expanding the use of genomic methods to include non-model species of conservation concern. We have developed a 96-marker SNP array for use in applied conservation monitoring of the Scandinavian wolverine (Gulo gulo) population. By genotyping more than a thousand non-invasively collected samples, we were able to obtain precise estimates of different types of genotyping errors and sample dropout rates. The SNP panel significantly outperforms the SSR markers (and DBY intron markers for sexing) both in terms of precision in genotyping, sex assignment and individual identification, as well as in the proportion of samples successfully genotyped. Furthermore, SNP genotyping offers a simplified laboratory and analysis pipeline with fewer samples needed to be repeatedly genotyped in order to obtain reliable consensus data. In addition, we utilised a unique opportunity to successfully demonstrate the application of SNP genotype data for reconstructing pedigrees in wild populations, by validating the method with samples from wild individuals with known relatedness. By offering a simplified workflow with improved performance, we anticipate this methodology will facilitate the use of non-invasive samples to improve genetic management of many different types of populations that have previously been challenging to survey. |
format |
Article in Journal/Newspaper |
author |
Ekblom, Robert Aronsson, Malin Elsner-Gearing, Franziska Johansson, Malin Fountain, Toby Persson, Jens |
author_facet |
Ekblom, Robert Aronsson, Malin Elsner-Gearing, Franziska Johansson, Malin Fountain, Toby Persson, Jens |
author_sort |
Ekblom, Robert |
title |
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples |
title_short |
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples |
title_full |
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples |
title_fullStr |
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples |
title_full_unstemmed |
Sample identification and pedigree reconstruction in Wolverine (Gulo gulo) using SNP genotyping of non-invasive samples |
title_sort |
sample identification and pedigree reconstruction in wolverine (gulo gulo) using snp genotyping of non-invasive samples |
publisher |
Uppsala universitet, Evolutionsbiologi |
publishDate |
2021 |
url |
http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-468631 https://doi.org/10.1007/s12686-021-01208-5 |
genre |
Gulo gulo |
genre_facet |
Gulo gulo |
op_relation |
Conservation Genetics Resources, 1877-7252, 2021, 13:3, s. 261-274 orcid:0000-0003-2222-1966 orcid:0000-0002-5501-4691 orcid:0000-0003-1405-7561 http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-468631 doi:10.1007/s12686-021-01208-5 ISI:000642384800001 |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.1007/s12686-021-01208-5 |
container_title |
Conservation Genetics Resources |
container_volume |
13 |
container_issue |
3 |
container_start_page |
261 |
op_container_end_page |
274 |
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1790601148935176192 |