Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides
Abstract All methods of diet analysis in marine mammals, including hard part analysis (HPA), have biases affecting the accuracy of prey‐species identification and frequency in the estimated diet due to differential consumption, digestion and retention. Using PCR amplification of specific prey DNA wi...
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Online Access: | http://dx.doi.org/10.1111/j.1755-0998.2009.02713.x https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fj.1755-0998.2009.02713.x https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1755-0998.2009.02713.x https://onlinelibrary.wiley.com/doi/full-xml/10.1111/j.1755-0998.2009.02713.x |
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crwiley:10.1111/j.1755-0998.2009.02713.x 2023-12-03T10:15:31+01:00 Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides MARSHALL, H. D. HART, K. A. YASKOWIAK, E. S. STENSON, G. B. McKINNON, D. PERRY, E. A. 2009 http://dx.doi.org/10.1111/j.1755-0998.2009.02713.x https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fj.1755-0998.2009.02713.x https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1755-0998.2009.02713.x https://onlinelibrary.wiley.com/doi/full-xml/10.1111/j.1755-0998.2009.02713.x en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology Resources volume 10, issue 1, page 181-189 ISSN 1755-098X 1755-0998 Genetics Ecology, Evolution, Behavior and Systematics Biotechnology journal-article 2009 crwiley https://doi.org/10.1111/j.1755-0998.2009.02713.x 2023-11-09T14:35:18Z Abstract All methods of diet analysis in marine mammals, including hard part analysis (HPA), have biases affecting the accuracy of prey‐species identification and frequency in the estimated diet due to differential consumption, digestion and retention. Using PCR amplification of specific prey DNA with species‐specific primers, we developed a DNA‐based method that complements HPA and provides an alternative means to detect prey from stomach contents of Harp Seals ( Pagophilus groenlandicus ). The target size that could be reliably amplified was determined using a digestion time‐series of Atlantic Cod ( Gadus morhua ) tissue in simulated seal stomachs. Various target lengths were trialed using general teleost primers; amplicons of approximately 800 bp or less were consistently obtained. Prey species‐specific PCR primers for Atlantic Cod, Arctic Cod ( Boreogadus saida ) and Capelin ( Mallotus villosus ) were designed and tested with DNA from the stomach contents of 31 Harp Seals. Amplicons were obtained for all three species‐specific primer sets. Amplification results compared with HPA revealed: (i) Atlantic Cod hard parts were found in five stomachs where no Atlantic Cod DNA amplified, suggesting that Atlantic Cod may be over‐represented in the estimated diet, (ii) amplification of Arctic Cod DNA occurred for 17 stomachs, including all 12 stomachs with, and five stomachs without, Arctic Cod hard parts, and (iii) Capelin DNA amplified for four of five stomachs with Capelin hard parts and for one stomach without Capelin hard parts. We conclude that PCR amplification of specific prey DNA provides a viable means to complement Harp Seal diet analysis by HPA, but suggest that valuable information for quantitative diet analysis rests in a quantitative PCR approach. Article in Journal/Newspaper Arctic cod Arctic atlantic cod Boreogadus saida Gadus morhua Harp Seal Pagophilus groenlandicus Wiley Online Library (via Crossref) Arctic Molecular Ecology Resources 10 1 181 189 |
institution |
Open Polar |
collection |
Wiley Online Library (via Crossref) |
op_collection_id |
crwiley |
language |
English |
topic |
Genetics Ecology, Evolution, Behavior and Systematics Biotechnology |
spellingShingle |
Genetics Ecology, Evolution, Behavior and Systematics Biotechnology MARSHALL, H. D. HART, K. A. YASKOWIAK, E. S. STENSON, G. B. McKINNON, D. PERRY, E. A. Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides |
topic_facet |
Genetics Ecology, Evolution, Behavior and Systematics Biotechnology |
description |
Abstract All methods of diet analysis in marine mammals, including hard part analysis (HPA), have biases affecting the accuracy of prey‐species identification and frequency in the estimated diet due to differential consumption, digestion and retention. Using PCR amplification of specific prey DNA with species‐specific primers, we developed a DNA‐based method that complements HPA and provides an alternative means to detect prey from stomach contents of Harp Seals ( Pagophilus groenlandicus ). The target size that could be reliably amplified was determined using a digestion time‐series of Atlantic Cod ( Gadus morhua ) tissue in simulated seal stomachs. Various target lengths were trialed using general teleost primers; amplicons of approximately 800 bp or less were consistently obtained. Prey species‐specific PCR primers for Atlantic Cod, Arctic Cod ( Boreogadus saida ) and Capelin ( Mallotus villosus ) were designed and tested with DNA from the stomach contents of 31 Harp Seals. Amplicons were obtained for all three species‐specific primer sets. Amplification results compared with HPA revealed: (i) Atlantic Cod hard parts were found in five stomachs where no Atlantic Cod DNA amplified, suggesting that Atlantic Cod may be over‐represented in the estimated diet, (ii) amplification of Arctic Cod DNA occurred for 17 stomachs, including all 12 stomachs with, and five stomachs without, Arctic Cod hard parts, and (iii) Capelin DNA amplified for four of five stomachs with Capelin hard parts and for one stomach without Capelin hard parts. We conclude that PCR amplification of specific prey DNA provides a viable means to complement Harp Seal diet analysis by HPA, but suggest that valuable information for quantitative diet analysis rests in a quantitative PCR approach. |
format |
Article in Journal/Newspaper |
author |
MARSHALL, H. D. HART, K. A. YASKOWIAK, E. S. STENSON, G. B. McKINNON, D. PERRY, E. A. |
author_facet |
MARSHALL, H. D. HART, K. A. YASKOWIAK, E. S. STENSON, G. B. McKINNON, D. PERRY, E. A. |
author_sort |
MARSHALL, H. D. |
title |
Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides |
title_short |
Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides |
title_full |
Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides |
title_fullStr |
Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides |
title_full_unstemmed |
Molecular identification of prey in the stomach contents of Harp Seals ( Pagophilus groenlandicus ) using species‐specific oligonucleotides |
title_sort |
molecular identification of prey in the stomach contents of harp seals ( pagophilus groenlandicus ) using species‐specific oligonucleotides |
publisher |
Wiley |
publishDate |
2009 |
url |
http://dx.doi.org/10.1111/j.1755-0998.2009.02713.x https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fj.1755-0998.2009.02713.x https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1755-0998.2009.02713.x https://onlinelibrary.wiley.com/doi/full-xml/10.1111/j.1755-0998.2009.02713.x |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic cod Arctic atlantic cod Boreogadus saida Gadus morhua Harp Seal Pagophilus groenlandicus |
genre_facet |
Arctic cod Arctic atlantic cod Boreogadus saida Gadus morhua Harp Seal Pagophilus groenlandicus |
op_source |
Molecular Ecology Resources volume 10, issue 1, page 181-189 ISSN 1755-098X 1755-0998 |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/j.1755-0998.2009.02713.x |
container_title |
Molecular Ecology Resources |
container_volume |
10 |
container_issue |
1 |
container_start_page |
181 |
op_container_end_page |
189 |
_version_ |
1784262425033310208 |