Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species.
Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically pe...
Published in: | Molecular Ecology Resources |
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Format: | Article in Journal/Newspaper |
Language: | English |
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Online Access: | https://serval.unil.ch/notice/serval:BIB_155D77B41AD3 https://doi.org/10.1111/1755-0998.13915 https://serval.unil.ch/resource/serval:BIB_155D77B41AD3.P001/REF.pdf http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_155D77B41AD31 |
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ftunivlausanne:oai:serval.unil.ch:BIB_155D77B41AD3 2024-02-11T10:02:48+01:00 Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. De Barba, M. Baur, M. Boyer, F. Fumagalli, L. Konec, M. Miquel, C. Pazhenkova, E. Remollino, N. Skrbinšek, T. Stoffel, C. Taberlet, P. application/pdf https://serval.unil.ch/notice/serval:BIB_155D77B41AD3 https://doi.org/10.1111/1755-0998.13915 https://serval.unil.ch/resource/serval:BIB_155D77B41AD3.P001/REF.pdf http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_155D77B41AD31 eng eng info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.13915 info:eu-repo/semantics/altIdentifier/pmid/38099394 info:eu-repo/semantics/altIdentifier/eissn/1755-0998 info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_155D77B41AD31 https://serval.unil.ch/notice/serval:BIB_155D77B41AD3 doi:10.1111/1755-0998.13915 urn:issn:1755-098X https://serval.unil.ch/resource/serval:BIB_155D77B41AD3.P001/REF.pdf http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_155D77B41AD31 info:eu-repo/semantics/openAccess CC BY 4.0 https://creativecommons.org/licenses/by/4.0/ Molecular Ecology Resources eDNA-based population studies high-throughput STR genotyping by sequencing individual identification large carnivores non-invasive genetics snow track sampling info:eu-repo/semantics/article article info:eu-repo/semantics/publishedVersion ftunivlausanne https://doi.org/10.1111/1755-0998.13915 2024-01-22T00:53:06Z Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR), and for brown bear a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear (5/7) and wolf (7/10) than for lynx (4/9), and locus genotyping success was greater for brown bear (0.88). The sex marker was typed in six out of seven brown bear samples. Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success, is needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA-based individual and population-level studies. Article in Journal/Newspaper Canis lupus Ursus arctos Lynx Lynx lynx lynx Université de Lausanne (UNIL): Serval - Serveur académique lausannois Molecular Ecology Resources |
institution |
Open Polar |
collection |
Université de Lausanne (UNIL): Serval - Serveur académique lausannois |
op_collection_id |
ftunivlausanne |
language |
English |
topic |
eDNA-based population studies high-throughput STR genotyping by sequencing individual identification large carnivores non-invasive genetics snow track sampling |
spellingShingle |
eDNA-based population studies high-throughput STR genotyping by sequencing individual identification large carnivores non-invasive genetics snow track sampling De Barba, M. Baur, M. Boyer, F. Fumagalli, L. Konec, M. Miquel, C. Pazhenkova, E. Remollino, N. Skrbinšek, T. Stoffel, C. Taberlet, P. Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. |
topic_facet |
eDNA-based population studies high-throughput STR genotyping by sequencing individual identification large carnivores non-invasive genetics snow track sampling |
description |
Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (Ursus arctos), European lynx (Lynx lynx) and wolf (Canis lupus). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR), and for brown bear a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear (5/7) and wolf (7/10) than for lynx (4/9), and locus genotyping success was greater for brown bear (0.88). The sex marker was typed in six out of seven brown bear samples. Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success, is needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA-based individual and population-level studies. |
format |
Article in Journal/Newspaper |
author |
De Barba, M. Baur, M. Boyer, F. Fumagalli, L. Konec, M. Miquel, C. Pazhenkova, E. Remollino, N. Skrbinšek, T. Stoffel, C. Taberlet, P. |
author_facet |
De Barba, M. Baur, M. Boyer, F. Fumagalli, L. Konec, M. Miquel, C. Pazhenkova, E. Remollino, N. Skrbinšek, T. Stoffel, C. Taberlet, P. |
author_sort |
De Barba, M. |
title |
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. |
title_short |
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. |
title_full |
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. |
title_fullStr |
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. |
title_full_unstemmed |
Individual genotypes from environmental DNA: Fingerprinting snow tracks of three large carnivore species. |
title_sort |
individual genotypes from environmental dna: fingerprinting snow tracks of three large carnivore species. |
url |
https://serval.unil.ch/notice/serval:BIB_155D77B41AD3 https://doi.org/10.1111/1755-0998.13915 https://serval.unil.ch/resource/serval:BIB_155D77B41AD3.P001/REF.pdf http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_155D77B41AD31 |
genre |
Canis lupus Ursus arctos Lynx Lynx lynx lynx |
genre_facet |
Canis lupus Ursus arctos Lynx Lynx lynx lynx |
op_source |
Molecular Ecology Resources |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1111/1755-0998.13915 info:eu-repo/semantics/altIdentifier/pmid/38099394 info:eu-repo/semantics/altIdentifier/eissn/1755-0998 info:eu-repo/semantics/altIdentifier/urn/urn:nbn:ch:serval-BIB_155D77B41AD31 https://serval.unil.ch/notice/serval:BIB_155D77B41AD3 doi:10.1111/1755-0998.13915 urn:issn:1755-098X https://serval.unil.ch/resource/serval:BIB_155D77B41AD3.P001/REF.pdf http://nbn-resolving.org/urn/resolver.pl?urn=urn:nbn:ch:serval-BIB_155D77B41AD31 |
op_rights |
info:eu-repo/semantics/openAccess CC BY 4.0 https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1111/1755-0998.13915 |
container_title |
Molecular Ecology Resources |
_version_ |
1790598861705707520 |