Combining hard-part and DNA analyses of scats with biologging and stable isotopes can reveal different diet compositions and feeding strategies within a fur seal population

Jeanniard‐du‐Dot, Tiphaine; Thomas, Austen C.; Cherel, Yves; Trites, Andrew W.; Guinet, Christophe

doi:10.3354/meps12381

Cited by 34 publications

(47 citation statements)

References 60 publications

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“…These approaches allow family-, genus-or species-level identifications, because there is an accurately curated barcode database (e.g. Jeanniard-du-Dot et al, 2017;Buglione et al, 2018). At present, DNA metabarcoding is a fast and simple alternative to traditional microscopy methods, because it allows the detection of prey DNA in digested samples and has been shown to be effective in recovering previously undetected prey groups (e.g.…”

Section: Introductionmentioning

confidence: 99%

DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco

Pereira

Xavier

Perera

et al. 2019

Biological Journal of the Linnean Society

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DNA metabarcoding is a fast and simple alternative to traditional microscopy methods, which have been the main tool for identification of prey in dietary studies of lizards. In this study, we applied a metabarcoding approach based on COI and 16S rRNA amplicons to assess diet partitioning and feeding strategies in three syntopic lizards from Taza, Morocco: Scelarcis perspicillata chabanaudi, Scelarcis perspicillata pellegrini and Podarcis vaucheri. In order to avoid competition, these lizards are expected to consume different prey species because they occupy distinct trophic niches, use different foraging strategies and express different dorsal pigmentation patterns. Given the spotted pattern of S. p. chabanaudi, we hypothesize a sit-and-wait foraging strategy with a less diverse diet and a higher consumption of mobile prey relative to the striped S. p. pellegrini and P. vaucheri which, as potential active foragers, are expected to have a higher diet diversity. Previous diet assessments using microscopy on faecal remains seem to contradict these expectations. Our results show that, as expected, the diet of S. p. chabanaudi is less diverse than the diet of S. p. pellegrini. Regarding P. vaucheri, our dietary data are consistent with the hypothesis that this species behaves as an active forager, owing to its high niche overlap with S. p. pellegrini. Advantages and limitations of molecular barcoding compared with the microscopy approach to the analysis of lizard diets are discussed.

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Section: Introductionmentioning

confidence: 99%

DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco

Pereira

Xavier

Perera

et al. 2019

Biological Journal of the Linnean Society

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“…Indeed, DNA barcoding is now acknowledged to address many of the problems inherent to morphological taxonomy, such as identifying cryptic species or linking different life stages (e.g., larvae) to a single species (Packer et al, ). Importantly, unlike morphological examination or stable isotopes, DNA barcoding can provide taxonomic resolution to the species level, allowing a more accurate description of the diversity of prey items (e.g., Granquist, Esparza‐Salas, Hauksson, Karlsson, & Angerbjörn, ; Jeanniard‐du‐Dot, Thomas, Cherel, Trites, & Guinet, ).…”

Section: Different Methodologies For the Assessment Of Trophic Interamentioning

confidence: 99%

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

2019

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Effective conservation of species and ecosystems requires the understanding of important ecological traits, such as dietary habits, food webs, and trophic niches. In diet studies, the visual identification of partially digested prey has been enhanced with the recent more powerful and accurate technique, DNA barcoding. Here, we summarize the contribution of this recent methodology to the investigation of both terrestrial and aquatic taxa diet, and compare the level of novelty uncovered through the use of this technique regarding species' ecology. From a total of 150 studies analyzed, focusing on more than 250 vertebrate wild species, seven domesticated taxa, and humans, we suggest that barcoding has led to more significant findings for aquatic taxa and ecosystems, where direct observations of feeding events and consequent trophic niche understanding are typically limited. Finally, we introduce the term dietary DNA (dDNA) to describe environmental approaches that use DNA extracted from gut, stomach, or fecal contents, aiming to assess both species dietary habits and describe local biodiversity. Particularly, we highlight the complementarity of environmental DNA (eDNA) and dDNA as a new tool for biodiversity assessments in remote areas, including most of the aquatic realm.

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“…The age class and body mass of the scat depositor are also unknown, both of which appear to be important factors influencing diet and foraging behavior (Bjorkland et al, 2015;Howard et al, 2013). One potential approach to address these limitations is to link movement studies of tagged individuals and scat analysis of their diet via genetic fingerprinting of samples to provide a full picture of diet and behavior (e.g., Jeanniard-du-Dot et al, 2017) and to refine bioenergetics models.…”

Section: Strengths and Limitationsmentioning

confidence: 99%

“…Questions regarding the foraging ecology of marine mammals are best examined by a combination of different techniques (e.g., Jeanniard-du-Dot, Thomas, Cherel, Trites, & Guinet, 2017). Here, we present a novel combination of noninvasive techniques that use scat DNA for both sex determination of the predator and high taxonomic resolution molecular bar coding of the prey.…”

mentioning

confidence: 99%

“…In this study, we performed DNA-bar coding analysis and qPCR on harbor seal fecal samples to determine the identity, estimate prey species proportions in diet, and the sex of the harbor seal, respectively. Other pinniped studies have used molecular techniques to determine the diet of one sex (Jeanniard-du-Dot et al, 2017;Peters et al, 2015) or the diet of the species without differentiating the sex (Hui, Morita, Kobayashi, Mitani, & Miyashita, 2017;Kvitrud, Riemer, Brown, Bellinger, & Banks, 2005;Parsons, Piertney, Middlemas, Hammond, & Armstrong, 2005;Thomas et al, 2017;Wright, Riemer, Brown, Ougzin, & Bucklin, 2007). To our knowledge, this is the first study in pinnipeds that incorporates these two molecular methods to differentiate males and females and estimate their diet from scat.…”

mentioning

confidence: 99%

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Large‐scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern

Schwarz

Spitzer

Thomas

et al. 2018

Ecology and Evolution

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Sex‐specific diet information is important in the determination of predator impacts on prey populations. Unfortunately, the diet of males and females can be difficult to describe, particularly when they are marine predators. We combined two molecular techniques to describe haul‐out use and prey preferences of male and female harbor seals (Phoca vitulina) from Comox and Cowichan Bay (Canada) during 2012–2013. DNA metabarcoding quantified the diet proportions comprised of prey species in harbor seal scat, and qPCR determined the sex of the individual that deposited each scat. Using 287 female and 260 male samples, we compared the monthly sex ratio with GLMs and analyzed prey consumption relative to sex, season, site, and year with PERMANOVA. The sex ratio between monthly samples differed widely in both years (range = 12%–79% males) and showed different patterns at each haul‐out site. Male and female diet differed across both years and sites: Females consumed a high proportion of demersal fish species while males consumed more salmonid species. Diet composition was related to both sex and season (PERMANOVA: R 2 = 27%, p < 0.001; R 2 = 24%, p < 0.001, respectively) and their interaction (PERMANOVA: R 2 = 11%, p < 0.001). Diet differences between males and females were consistent across site and year, suggesting fundamental foraging differences, including that males may have a larger impact on salmonids than females. Our novel combination of techniques allowed for both prey taxonomic and spatiotemporal resolution unprecedented in marine predators.

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Combining hard-part and DNA analyses of scats with biologging and stable isotopes can reveal different diet compositions and feeding strategies within a fur seal population

Cited by 34 publications

References 60 publications

DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco

DNA metabarcoding to assess diet partitioning and feeding strategies in generalist vertebrate predators: a case study on three syntopic lacertid lizards from Morocco

DNA metabarcoding in diet studies: Unveiling ecological aspects in aquatic and terrestrial ecosystems

Large‐scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern

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