Using quantitative real-time PCR to detect salmonid prey in scats of grey Halichoerus grypus and harbour Phoca vitulina seals in Scotland: an experimental and field study

Iveta Matejusova, Fiona Doig, Stuart Middlemas, S MacKay, Alex Douglas, J Armstrong, Carey Cunningham, M Snow

Research output: Contribution to journalArticle

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Abstract

There is considerable debate over the impact of seal predation on salmonid populations in both the Atlantic and Pacific oceans. Conventional hard-part analysis of scats has suggested that salmonids represent a minor component of the diet of grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina) in the UK. However, it is unclear whether this is an accurate reflection of the diet or due to methodological problems. To investigate this issue, we applied quantitative PCR (qPCR) to examine the presence of salmonids in the diet of seals in the Moray Firth, UK, during the summers of 2003 and 2005.

Two qPCR assays were designed to detect Atlantic salmon Salmo salar and sea trout Salmo trutta DNA in field samples and experimentally spiked scats. The proportion of scats sampled in the field that were positive for salmonid DNA was low (ª10%). However, the DNA technique consistently resulted in more positive scats than when hard-part analysis was used.

An experimental study using spiked scat material revealed a highly significant negative relationship between Ct values obtained from the Atlantic salmon qPCR assay and the proportion of Atlantic salmon material added to scats. The Ct value denotes the cycle number at which the increasing fluorescence signal of target DNA crosses a threshold value. Ct values from field-collected seal scats suggested they contained a very low concentration of salmonid remains (1–5%) based on an approximate calibration curve constructed from the experimental data.

Synthesis and applications. The qPCR assay approach was shown to be highly efficient and consistent in detection of salmonids from seal scats, and to be more sensitive than conventional hard-parts analysis. Nevertheless, our results confirm previous studies indicating that salmonids are not common prey for seals in these Scottish estuaries. These studies support current management practice, which focuses on control of the small number of seals that move into key salmonid rivers, rather than targeting the larger groups of animals that haul-out in nearby estuaries
Original languageEnglish
Pages (from-to)632 - 640
Number of pages9
JournalJournal of Applied Ecology
Volume45
Issue number2
DOIs
Publication statusPublished - Apr 2008

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salmonid
harbor
experimental study
DNA
assay
diet
estuary
feces
targeting
management practice
fluorescence
predation
calibration
field study
animal
ocean
summer
river
analysis
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Using quantitative real-time PCR to detect salmonid prey in scats of grey Halichoerus grypus and harbour Phoca vitulina seals in Scotland : an experimental and field study. / Matejusova, Iveta; Doig, Fiona; Middlemas, Stuart; MacKay, S; Douglas, Alex; Armstrong, J; Cunningham, Carey; Snow, M.

In: Journal of Applied Ecology, Vol. 45, No. 2, 04.2008, p. 632 - 640.

Research output: Contribution to journalArticle

Matejusova, Iveta ; Doig, Fiona ; Middlemas, Stuart ; MacKay, S ; Douglas, Alex ; Armstrong, J ; Cunningham, Carey ; Snow, M. / Using quantitative real-time PCR to detect salmonid prey in scats of grey Halichoerus grypus and harbour Phoca vitulina seals in Scotland : an experimental and field study. In: Journal of Applied Ecology. 2008 ; Vol. 45, No. 2. pp. 632 - 640.
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abstract = "There is considerable debate over the impact of seal predation on salmonid populations in both the Atlantic and Pacific oceans. Conventional hard-part analysis of scats has suggested that salmonids represent a minor component of the diet of grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina) in the UK. However, it is unclear whether this is an accurate reflection of the diet or due to methodological problems. To investigate this issue, we applied quantitative PCR (qPCR) to examine the presence of salmonids in the diet of seals in the Moray Firth, UK, during the summers of 2003 and 2005. Two qPCR assays were designed to detect Atlantic salmon Salmo salar and sea trout Salmo trutta DNA in field samples and experimentally spiked scats. The proportion of scats sampled in the field that were positive for salmonid DNA was low (ª10{\%}). However, the DNA technique consistently resulted in more positive scats than when hard-part analysis was used. An experimental study using spiked scat material revealed a highly significant negative relationship between Ct values obtained from the Atlantic salmon qPCR assay and the proportion of Atlantic salmon material added to scats. The Ct value denotes the cycle number at which the increasing fluorescence signal of target DNA crosses a threshold value. Ct values from field-collected seal scats suggested they contained a very low concentration of salmonid remains (1–5{\%}) based on an approximate calibration curve constructed from the experimental data. Synthesis and applications. The qPCR assay approach was shown to be highly efficient and consistent in detection of salmonids from seal scats, and to be more sensitive than conventional hard-parts analysis. Nevertheless, our results confirm previous studies indicating that salmonids are not common prey for seals in these Scottish estuaries. These studies support current management practice, which focuses on control of the small number of seals that move into key salmonid rivers, rather than targeting the larger groups of animals that haul-out in nearby estuaries",
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T2 - an experimental and field study

AU - Matejusova, Iveta

AU - Doig, Fiona

AU - Middlemas, Stuart

AU - MacKay, S

AU - Douglas, Alex

AU - Armstrong, J

AU - Cunningham, Carey

AU - Snow, M

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N2 - There is considerable debate over the impact of seal predation on salmonid populations in both the Atlantic and Pacific oceans. Conventional hard-part analysis of scats has suggested that salmonids represent a minor component of the diet of grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina) in the UK. However, it is unclear whether this is an accurate reflection of the diet or due to methodological problems. To investigate this issue, we applied quantitative PCR (qPCR) to examine the presence of salmonids in the diet of seals in the Moray Firth, UK, during the summers of 2003 and 2005. Two qPCR assays were designed to detect Atlantic salmon Salmo salar and sea trout Salmo trutta DNA in field samples and experimentally spiked scats. The proportion of scats sampled in the field that were positive for salmonid DNA was low (ª10%). However, the DNA technique consistently resulted in more positive scats than when hard-part analysis was used. An experimental study using spiked scat material revealed a highly significant negative relationship between Ct values obtained from the Atlantic salmon qPCR assay and the proportion of Atlantic salmon material added to scats. The Ct value denotes the cycle number at which the increasing fluorescence signal of target DNA crosses a threshold value. Ct values from field-collected seal scats suggested they contained a very low concentration of salmonid remains (1–5%) based on an approximate calibration curve constructed from the experimental data. Synthesis and applications. The qPCR assay approach was shown to be highly efficient and consistent in detection of salmonids from seal scats, and to be more sensitive than conventional hard-parts analysis. Nevertheless, our results confirm previous studies indicating that salmonids are not common prey for seals in these Scottish estuaries. These studies support current management practice, which focuses on control of the small number of seals that move into key salmonid rivers, rather than targeting the larger groups of animals that haul-out in nearby estuaries

AB - There is considerable debate over the impact of seal predation on salmonid populations in both the Atlantic and Pacific oceans. Conventional hard-part analysis of scats has suggested that salmonids represent a minor component of the diet of grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina) in the UK. However, it is unclear whether this is an accurate reflection of the diet or due to methodological problems. To investigate this issue, we applied quantitative PCR (qPCR) to examine the presence of salmonids in the diet of seals in the Moray Firth, UK, during the summers of 2003 and 2005. Two qPCR assays were designed to detect Atlantic salmon Salmo salar and sea trout Salmo trutta DNA in field samples and experimentally spiked scats. The proportion of scats sampled in the field that were positive for salmonid DNA was low (ª10%). However, the DNA technique consistently resulted in more positive scats than when hard-part analysis was used. An experimental study using spiked scat material revealed a highly significant negative relationship between Ct values obtained from the Atlantic salmon qPCR assay and the proportion of Atlantic salmon material added to scats. The Ct value denotes the cycle number at which the increasing fluorescence signal of target DNA crosses a threshold value. Ct values from field-collected seal scats suggested they contained a very low concentration of salmonid remains (1–5%) based on an approximate calibration curve constructed from the experimental data. Synthesis and applications. The qPCR assay approach was shown to be highly efficient and consistent in detection of salmonids from seal scats, and to be more sensitive than conventional hard-parts analysis. Nevertheless, our results confirm previous studies indicating that salmonids are not common prey for seals in these Scottish estuaries. These studies support current management practice, which focuses on control of the small number of seals that move into key salmonid rivers, rather than targeting the larger groups of animals that haul-out in nearby estuaries

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JO - Journal of Applied Ecology

JF - Journal of Applied Ecology

SN - 0021-8901

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