A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare

Buglione, Maria; Maselli, Valeria; Rippa, Daniela; Filippo, Gabriele de; Trapanese, Martina; Fulgione, Domenico

doi:10.1016/j.mambio.2017.10.010

Cited by 43 publications

(38 citation statements)

References 59 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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“…DNA metabarcoding has emerged as a novel method for diet analysis because of the ability to reveal rare or difficult to identify species (Shehzad et al 2012, De Barba et al 2014, Berry et al 2015, Srivathsan et al 2015, Kartzinel et al 2015, McInnes et al 2017, Buglione et al 2018). However, substantial uncertainty remains as to whether inference from mechanical sorting and DNA metabarcoding produce comparable results, particularly if scats are of uncertain age and quality.…”

Section: Discussionmentioning

confidence: 99%

Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

Massey¹,

Roffler²,

Vermeul³

et al. 2019

Preprint

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1DNA metabarcoding has become a powerful technique for identifying species and 2 profiling biodiversity with the potential to improve efficiency, reveal rare prey species, and 3 correct mistaken identification error in diet studies. However, the extent to which molecular 4 approaches agree with traditional approaches is unknown for many species. Here, we compare 5 diets from wolf scats profiled using both mechanical sorting and metabarcoding of amplified 6 vertebrate DNA sequences. Our objectives were: (1) compare findings from mechanical sorting 7 and metabarcoding as a method of diet profiling and (2) use results to better understand diets of 8 wolves on Prince of Wales Island, a population of conservation concern. We predicted 9 metabarcoding would reveal both higher diversity of prey and identify rare species that are 1 0 overlooked with mechanical sorting. We also posited that the relative contribution of Sitka black-1 1 tailed deer (Odocoileus hemionus sitkensis) and beaver (Castor canadensis) would be 1 2 overestimated with mechanical sorting methods because of the failure to account for the full diet 1 3 diversity of these wolves. We found that there was substantial overlap in the diets revealed using 1 4 both methods, indicating that deer, beaver, and black bear (Ursus americanus) were the primary 1 5 prey species. However, there was a large discrepancy in the occurrence of beaver in scats (54% 1 6 and 24% from mechanical sorting and metabarcoding, respectively) explained by the high rate of 1 7 false positives with mechanical sorting methods. Metabarcoding revealed more diet diversity 1 8 than mechanical sorting, thus supporting our initial predictions. Prince of Wales Island wolves

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“…Coupled with next-generation sequencing (NGS), DNA metabarcoding technology can sequence many samples in a high-throughput and cost-effective fashion and reveal the entire taxonomic composition of thousands of samples simultaneously . This new molecular approach has been successfully applied for the diet analyses of various species, including carnivores (Berry et al, 2017;Smith, Thomas, Levi, Wang, & Wilmers, 2018), omnivores (De Barba et al, 2013;Robeson et al, 2017), herbivores (Kartzinel et al, 2015), small mammals (Buglione et al, 2018), lizards (Moreno-Rueda, Melero, Reguera, Zamora-Camacho, & Álvarez-Benito, 2017), birds (Sullins et al, 2018) and invertebrates (Hawlitschek, Fernández-González, Balmori-de la Puente, & Castresana, 2018;Kamenova, Bretagnolle, Plantegenest, & Canard, 2018).…”

Section: Introductionmentioning

confidence: 99%

Prey partitioning between sympatric canid species revealed by DNA metabarcoding

Shi

Hoareau

Reese

et al. 2019

Preprint

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The recovery of apex predators relies on restoring the full suite of trophic interactions within the ecosystem. Diet analysis with DNA metabarcoding technology can help deliver insights into these trophic interactions with fine-grained resolution. The recovery of wolves in Washington state offers an excellent case to study the trophic cascade impacts of the apex predators on the ecosystem and explore prey partitioning between sympatric canid species. We used DNA metabarcoding technology on scats to characterize the diet composition and its spatiotemporal variations of wolves and coyotes and quantified the diet niche overlap between these two canid species in northeastern Washington. In total, 19 different prey taxa were detected. Frequency of occurrence data showed that wolves primarily preyed upon deer (Odocoileus sp.) (47.47%) and moose (Alces alces) (42.42%). Coyotes also consumed moose (30.10%) and deer (21.36%), but snowshoe hares (Lepus americanus) were the most common prey (61.17%) in their diet. There were significant spatial variations in the wolf diet composition (p = 0.001) with wolves in the Dirty Shirt pack range consuming more moose (71.43%). Coyotes showed significant spatial and temporal dietary variations (season: p = 0.037; pack: p = 0.003; pack:season p = 0.043). Our data suggested that coyotes use ungulate carrion subsidies from wolves as food resources. DNA metabarcoding with fecal DNA provides an excellent noninvasive tool to characterize diet profile at the fine-grained level and can be applied to other carnivore species to help understand the impacts of recovery of apex predators on the local ecosystems.

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A pilot study on the application of DNA metabarcoding for non-invasive diet analysis in the Italian hare

Cited by 43 publications

References 59 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

Comparison of mechanical sorting and DNA metabarcoding for diet analysis with degraded wolf scats

Prey partitioning between sympatric canid species revealed by DNA metabarcoding

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