Pacific harbor seals (Phoca vitulina) and salmon: genetics presents hard numbers for elucidating predator-prey dynamics

Kvitrud, M. A.; Riemer, Susan D.; Brown, Robin F.; Bellinger, M. Renee; Banks, Michael

doi:10.1007/s00227-005-0047-9

Cited by 28 publications

(27 citation statements)

References 16 publications

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“…() and Kvitrud et al . () who concluded it was probably due to differences in the DNA template for each run. This indicates that there is some stochasticity involved, which may have been exacerbated by relatively small subgroup sample sizes, a known issue with this type of data collection (Greenstone et al .…”

Section: Discussionmentioning

confidence: 99%

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Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA‐based diet analyses

Egeter

Bishop

Robertson

2014

Molecular Ecology Resources

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Amphibians are currently the most threatened group of vertebrates worldwide, and introduced fauna play a major role in their decline. The control of introduced predators to protect endangered species is often based on predation rates derived from diet studies of predators, but prey detection probabilities using different techniques are variable. We measured the detectability of frogs as prey, using morphological and DNA-based diet analyses, in the stomachs and faeces of four mammal species that have been introduced to many areas of the world. Frogs (Litoria raniformis) were fed to rats (Rattus norvegicus and R. rattus), mice (Mus musculus) and hedgehogs (Erinaceus europaeus). DNA-based analysis outperformed morphological analysis, increasing the prey detection rate from 2% to 70% in stomachs and from 0% to 53% in faeces. In most cases, utilizing either stomachs or faeces did not affect the success of prey DNA detection; however, using faeces extended the detectability half-life from 7 to 21 h. This study is the first to measure prey DNA detection periods in mammalian stomachs, and the first to compare prey DNA detection periods in the stomachs and faeces of vertebrates. The results indicate that DNA-based diet analysis provides a more reliable approach for detecting amphibians as prey and has the potential to be used to estimate the rate of predation by introduced mammals on endangered amphibians.

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Section: Discussionmentioning

confidence: 99%

“…; Kvitrud et al . ). Designated nonadjacent areas of the laboratory were used for pre‐ and post‐PCR procedures (see Appendix S4, Supporting information for details of individual feeding trials and prey identification outcomes for individual stomach and faecal samples).…”

Section: Methodsmentioning

confidence: 97%

Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA‐based diet analyses

Egeter

Bishop

Robertson

2014

Molecular Ecology Resources

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“…The majority of genetic diet studies carried out on vertebrates have focused on identification of prey tissue remains recovered from stomach contents [e.g. 9], [18] or hard parts in faeces [19], [20]. The approach has also been applied to more highly processed amorphous faecal material in some instances [e.g.…”

Section: Introductionmentioning

confidence: 99%

Studying Seabird Diet through Genetic Analysis of Faeces: A Case Study on Macaroni Penguins (Eudyptes chrysolophus)

et al. 2007

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BackgroundDetermination of seabird diet usually relies on the analysis of stomach-content remains obtained through stomach flushing; this technique is both invasive and logistically difficult. We evaluate the usefulness of DNA-based faecal analysis in a dietary study on chick-rearing macaroni penguins (Eudyptes chrysolophus) at Heard Island. Conventional stomach-content data was also collected, allowing comparison of the approaches.Methodology/Principal FindingsPrey-specific PCR tests were used to detect dietary DNA in faecal samples and amplified prey DNA was cloned and sequenced. Of the 88 faecal samples collected, 39 contained detectable DNA from one or more of the prey groups targeted with PCR tests. Euphausiid DNA was most commonly detected in the early (guard) stage of chick-rearing, and detection of DNA from the myctophid fish Krefftichthys anderssoni and amphipods became more common in samples collected in the later (crèche) stage. These trends followed those observed in the penguins' stomach contents. In euphausiid-specific clone libraries the proportion of sequences from the two dominant euphausiid prey species (Euphausia vallentini and Thysanoessa macrura) changed over the sampling period; again, this reflected the trend in the stomach content data. Analysis of prey sequences in universal clone libraries revealed a higher diversity of fish prey than identified in the stomachs, but non-fish prey were not well represented.Conclusions/SignificanceThe present study is one of the first to examine the full breadth of a predator's diet using DNA-based faecal analysis. We discuss methodological difficulties encountered and suggest possible refinements. Overall, the ability of the DNA-based approach to detect temporal variation in the diet of macaroni penguins indicates this non-invasive method will be generally useful for monitoring population-level dietary trends in seabirds.

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“…It is unclear whether this is due to salmonids forming a small part of the diet, or the result of salmonid otoliths being under‐represented compared with those of other species (Boyle, Pierce & Diack 1990). An additional problem occurs where it is difficult to distinguish between closely related salmonid species once the hard parts have been subject to digestion (Kvitrud et al . 2005; Middlemas et al .…”

Section: Introductionmentioning

confidence: 99%

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

Matějusová

Doig

Middlemas

et al. 2007

Journal of Applied Ecology

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Summary 1.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. 2. 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 ( ≈ 10%). However, the DNA technique consistently resulted in more positive scats than when hard-part analysis was used.3. 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. 4. 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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Pacific harbor seals (Phoca vitulina) and salmon: genetics presents hard numbers for elucidating predator-prey dynamics

Cited by 28 publications

References 16 publications

Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA‐based diet analyses

Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA‐based diet analyses

Studying Seabird Diet through Genetic Analysis of Faeces: A Case Study on Macaroni Penguins (Eudyptes chrysolophus)

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

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