Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition?

Deagle, Bruce E.; Tollit, Dominic J.

doi:10.1007/s10592-006-9197-7

Cited by 143 publications

(142 citation statements)

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“…There is currently no precise way to quantify prey in the stomach using metabarcoding. Unfortunately, it cannot be assumed that the number of sequences for each particular species represents the amount of DNA (or number of individuals) contributing to the sample because the quality of that DNA depends on many factors including degradation and digestion rates (Deagle & Tollit 2007, Troedsson et al 2009, Valentini et al 2009b). Thus, quantitative analyses at this time are limited to the frequency of prey occurrence.…”

Section: Discussionmentioning

confidence: 99%

“…Results are limited or biased to the frequency of occurrence, which still provides useful information when seeking to understand localized effects of an invasive predator. However, the underlying variability in DNA quality, differential breakdown of that DNA during digestion, and differences in digestion stages (Deagle & Tollit 2007, Troedsson et al 2009, Valentini et al 2009b, as well as the objective of identifying several different organisms within the same sample (i.e. the gut) (Valentini et al 2009a), still hinder the quantification aspect in metabarcoding of gut contents.…”

Section: Introductionmentioning

confidence: 99%

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Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

Harms-Tuohy¹,

Schizas²,

Appeldoorn³

2016

Mar. Ecol. Prog. Ser.

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Studies of lionfish feeding ecology seek to document the ecological impact of this invasive predatory species and determine which native prey species are at greatest risk. There are 2 common approaches to feeding ecology through gut content analysis: morphological identification to the lowest possible taxonomic rank and/or DNA barcoding of individual prey components in the stomach. The major disadvantage of both techniques is their inability to use advanced digested material. This study introduces next-generation sequencing to lionfish feeding ecology, employing DNA metabarcoding to analyze all components of the gut contents, including the previously unidentifiable portion. Sixty-three lionfish were caught from the inshore and offshore reefs of La Parguera, Puerto Rico. Stomach contents were separated into 2 sample componentsa liquid (i.e. digested) and undigested tissue. A 313 bp region of the cytochrome oxidase subunit I (COI) gene was amplified from extracted DNA using specific primers for Caribbean reef fish. Samples were sequenced with an Illumina MiSeq platform, and the resulting 950+ sequences were compared against GenBank and the Barcode of Life Database to identify specimens at the lowest taxonomic level. Thirty-nine fish species from 16 families were identified (35 each in the digested and tissue fractions), including members of Pomacentridae, Acanthuridae, Gobiidae, Apogonidae, and Scaridae. Using the digested liquiform material proved efficient in detecting prey species, especially those that would have been missed with traditional methods.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

Harms-Tuohy¹,

Schizas²,

Appeldoorn³

2016

Mar. Ecol. Prog. Ser.

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“…Direct quantification of prey consumption using amplicon numbers is not recommended because of potential differences in digestibility, individual size and amounts of mitochondrial DNA per gram of tissues from different prey species (Deagle et al, 2010). A few studies have shown that the proportion of prey species' DNA retrieved from predator faecal samples and amplified by qPCR can be somewhat representative of the proportion of biomass eaten (Deagle & Tollit, 2007;Bowles et al, 2011). And these sequence counts have been used as semiquantitative measures of the biomass of prey eaten (Deagle et al, 2009).…”

Section: Accepted Manuscriptmentioning

confidence: 99%

“…One issue with their proposed method is that large quantities of DNA from one live specimen accidentally taken in one of their 0.5 kg soil cores could dominate the PCR process (Deagle & Tollit, 2007) and mask the presence of other species, or at least result in a biased representation of species abundance. Such bias could be minimised by collecting several small soil cores and mixing them together to make a more representative sample (Taberlet et al, 2012).…”

Section: Boxes Tables and Ifguresmentioning

confidence: 99%

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

2015

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“…2008a,b). Given the vast distances that lactating New Zealand fur seals travel to forage, interpreting diet using traditional methods is unlikely to accurately represent the diet of seals foraging in distant oceanic waters, or provide a means by which to detect and quantify the spatial separation of foraging habitats.Owing to such shortcomings, biochemical and molecular methods are increasingly being used to complement traditional methods in validating and/or providing information on dietary preferences of marine mammals (Iverson et al 1997, Cherel et al 2000, Deagle & Tollit 2007. One such technique is fatty acid (FA) analysis.…”

mentioning

confidence: 99%

Milk fatty acids predict the foraging locations of the New Zealand fur seal: continental shelf versus oceanic waters

Baylis

Nichols

2009

Mar. Ecol. Prog. Ser.

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Lactating New Zealand fur seals Arctocephalus forsteri utilise 2 ecological regions: continental shelf habitats and oceanic habitats associated with the Subtropical Front. Using milk fatty acids (FA) obtained from 29 satellite-tracked fur seals, we characterised the FA composition of seals that foraged on the continental shelf, and those that foraged in oceanic waters. Seals that foraged within oceanic waters were characterised by milk being comparatively high in monounsaturated fatty acids (MUFA; 47.4 ± 4.4%, mean ± SD), and lower in polyunsaturated fatty acids (PUFA; 23.8 ± 4.0%) when compared to seals that foraged in continental shelf waters (MUFA 36.7 ± 5.4 and PUFA 31.4 ± 5.5%). Based on FA compositions, we predicted the likelihood that milk samples collected at random (n = 131) represented individual seals having foraged either on the continental shelf or in distant oceanic waters. Results indicated that 74% (n = 97) of seals were likely to have foraged in oceanic waters, with 26% (n = 34) likely to have foraged within continental shelf waters. These results were supported by the small sub-sample of 29 satellite-tracked seals, which indicated that 62% of seals had foraged in oceanic waters. FA analysis and satellite-tracking results contrasted with scat analyses, from which only 7% of scats contained prey remains from oceanic waters. The results suggest scats were biased toward females foraging on the continental shelf. To further understand the diet of New Zealand fur seals, additional information on potential prey species that inhabit waters associated with the Subtropical Front south of Australia is required, as well as the continued development and application of alternative dietary techniques. KEY WORDS: Milk fatty acids · New Zealand fur seal · Subtropical Front · Continental shelf Resale or republication not permitted without written consent of the publisherMar Ecol Prog Ser 380: [271][272][273][274][275][276][277][278][279][280][281][282][283][284][285][286] 2009 sent diet and to assess trophic interactions, the ability to separate dietary information from different ecological regions utilised by marine predators is required.Traditionally the diets of marine predators have been largely inferred using scat, regurgitation and stomach samples. Although these methods have proven to be invaluable, it is often assumed they are only representative of the last foraging bout, and inherent biases associated with differences in the rates of passage of food through the gut and in the digestibility of particular prey are well established (Dellinger & Trillmich 1988, Bodley et al. 1999, Staniland 2002. As such, the accuracy at which traditional methods are able to reconstruct the diet of wide-ranging marine predators is dependant, to some degree, on the characteristics of their foraging trips (such as distance and duration), which vary temporally (i.e. seasonal) and spatially (colony location) and between individuals (e.g. Beauplet et al. 2004, Gremillet et al. 2004, Robson et al. 2004, Staniland et...

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Quantitative analysis of prey DNA in pinniped faeces: potential to estimate diet composition?

Cited by 143 publications

References 13 publications

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats

Milk fatty acids predict the foraging locations of the New Zealand fur seal: continental shelf versus oceanic waters

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