Unraveling the dietary diversity of Neotropical top predators using scat DNA metabarcoding: A case study on the elusive Giant Otter

Quéméré, Erwan; Aucourd, Marie; Troispoux, Valérie; Brosse, Sébastien; Murienne, Jérôme; Covain, Raphaël; Bail, Pierre‐Yves Le; Olivier, J. Hardy; Tysklind, Niklas; Galan, Maxime

doi:10.1002/edn3.195

Cited by 12 publications

(7 citation statements)

References 74 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our diagnostic method with species-specific markers adds to the more frequent studies using DNA from carnivore scats to identify prey (Hacker et al, 2021;Quéméré et al, 2021;Roffler et al, 2021;Shi et al, 2021;Smith et al, 2018;Xiong et al, 2017). These studies primarily used DNA metabarcoding, which produces a vast amount of valuable information but sometimes also needs consideration of potential bias sources in key steps in the data handling process, lack of reference databases of barcodes for many prey species, but also intensive laboratory procedures and considerable bioinformatics training (Hacker et al, 2021;Tercel et al, 2021;Zinger et al, 2019).…”

Section: Discussionmentioning

confidence: 99%

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Bernardi

Wikenros

Hedmark

et al. 2021

Ecology and Evolution

View full text Add to dashboard Cite

Large carnivore feeding ecology plays a crucial role for management and conservation for predators and their prey. One of the keys to this kind of research is to identify the species composition in the predator diet, for example, prey determination from scat content. DNA‐based methods applied to detect prey in predators’ scats are viable alternatives to traditional macroscopic approaches, showing an increased reliability and higher prey detection rate. Here, we developed a molecular method for prey species identification in wolf (Canis lupus) scats using multiple species‐specific marker loci on the cytochrome b gene for 18 target species. The final panel consisted of 80 assays, with a minimum of four markers per target species, and that amplified specifically when using a high‐throughput Nanofluidic array technology (Fluidigm Inc.). As a practical example, we applied the method to identify target prey species DNA in 80 wolf scats collected in Sweden. Depending on the number of amplifying markers required to obtain a positive species call in a scat, the success in determining at least one prey species from the scats ranged from 44% to 92%. Although we highlight the need to evaluate the optimal number of markers for sensitive target species detection, the developed method is a fast and cost‐efficient tool for prey identification in wolf scats and it also has the potential to be further developed and applied to other areas and large carnivores as well.

show abstract

Section: Discussionmentioning

confidence: 99%

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Bernardi

Wikenros

Hedmark

et al. 2021

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…Using a single set of primers focusing on specific prey groups may produce biased results (Clarke et al, 2014;Piñol et al, 2015). The use of multiple primers should minimize such bias and produce a more comprehensive result (Alberdi et al, 2018;Quéméré et al, 2021). In our study, although slightly different prey taxa were detected when lower thresholds were applied, no difference in prey taxon richness and composition was found between the two sets of primers (Figures 2A,B and Supplementary Figures 2-4), indicating that both primer sets produced a reliable list of the main prey taxa.…”

Section: Discussionmentioning

confidence: 99%

“…Different primers may focus on different taxa and using a single universal primer influences what prey species can be identified by this method (Da Silva et al, 2019). Thus, multi-primer metabarcoding is required to reveal a complete diet (Da Silva et al, 2019;Quéméré et al, 2021). For predators that have relatively simple diets (e.g., snow leopard has 10 prey species; Weiskopf et al, 2016) a single primer may be sufficient to reveal their main prey taxa (Browett et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…Analyses of otter diet have traditionally been based on morphological identification of undigested prey remains in spraints, usually at a higher taxonomic level than the prey species (Kruuk et al, 1994;Remonti et al, 2010;Reid et al, 2013). Recently, otter researchers have turned to DNA metabarcoding to obtain more accurate prey information, e.g., Eurasian otters (Thalinger et al, 2016;Hong et al, 2019;Kumari et al, 2019;Buglione et al, 2020;Harper et al, 2020;Marcolin et al, 2020;Jang-Liaw, 2021), and giant otters (Pteronura brasiliensis) (Quéméré et al, 2021). In China, the once widespread Eurasian otter populations declined nationwide between the 1950s and 1980s because they were widely harvested (Li and Chan, 2018).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Assessing the Diet of a Predator Using a DNA Metabarcoding Approach

Wang

Zheng

et al. 2022

Front. Ecol. Evol.

View full text Add to dashboard Cite

The diet of top predators is vital information needed to determine their ecological function and for their conservation management. However, the elusive habit and low population density of many predators constrains determination of their diets. While the morphological identification of scat contents is the traditional method, DNA metabarcoding has lately proven a more efficient and accurate method of identifying prey taxa. We applied DNA metabarcoding to analyzing the diet of the Eurasian otter (Lutra lutra), a top predator in freshwater ecosystems, using 12S and 16S rRNA mitochondrial primers target vertebrate prey. Diet did not vary among different data removal thresholds of 0.1, 1, 3, and 5%, comprising fishes (>90%), amphibians and birds (>2%), and occasionally mammals (<2%). Both 12S and 16S primers revealed similar otter diets, indicating that a single set of primers with a higher threshold is cost-effective for detecting the main prey taxa. Using 12S primers and a 5% threshold, we found no seasonal variation of otter diet in the Tangjiahe National Nature Reserve. A different prey community was found outside the reserve, which resulted in different prey composition for otters. However, prey taxon richness was not different between otters in- and outside the reserve. Otters preferred Schizothorax spp., the largest-sized fish species in the reserve, whereas they mainly preyed on Triplophysa bleekeri, a small-sized fish species, outside the reserve. Otters’ flexible feeding strategy reflect their high adaptability. However, greater human disturbance outside the reserve may present significant challenges to otters by altering prey communities and reducing prey profitability. Combining fecal DNA metabarcoding and local fish survey will provide opportunities for more detailed studies on the impact of different levels of human disturbances on prey communities and otters.

show abstract

“…Analyses of scats provide a useful approach to indirectly analyse animal diets and species interactions (Kohn and Wayne, 1997), with DNA metabarcoding methods able to identify even heavily digested or microscopic taxa (de Barba et al, 2014;Kartzinel et al, 2015;Srivathsan et al, 2015;O'Rourke et al, 2020). Due to these advantages, scat metabarcoding is increasingly being used as tool in wildlife management (e.g., Young et al, 2020;Huang et al, 2021;Quéméré et al, 2021;Querejeta et al, 2022).…”

Section: Introductionmentioning

confidence: 99%

Ancient and modern scats record broken ecological interactions and a decline in dietary breadth of the critically endangered kākāpō parrot (Strigops habroptilus)

et al. 2023

View full text Add to dashboard Cite

Threatened animal taxa are often absent from most of their original habitats, meaning their ecological niche cannot be fully captured by contemporary data alone. Although DNA metabarcoding of scats and coprolites (palaeofaeces) can identify the past and present species interactions of their depositors, the usefulness of coprolites in conservation biology is untested as few endangered taxa have known coprolite records. Here, we perform multilocus metabarcoding sequencing and palynological analysis of dietary plants of >100 coprolites (estimated to date from c. 400–1900 A.D.) and > 100 frozen scats (dating c. 1950 A.D. to present) of the critically endangered, flightless, herbivorous kākāpō (Strigops habroptilus), a species that disappeared from its natural range in Aotearoa-New Zealand (NZ) after the 13th C. A.D. We identify 24 orders, 56 families and 67 native plant genera unrecorded in modern kākāpō diets (increases of 69, 108 and 75% respectively). We found that southern beeches (Nothofagaceae), which are important canopy-forming trees and not an important kākāpō food today, dominated kākāpō diets in upland (c. >900 m elevation) habitats. We also found that kākāpō frequently consumed hemiparasitic mistletoes (Loranthaceae) and the holoparasitic wood rose (Dactylanthus taylorii), taxa which are nutrient rich, and now threatened by mammalian herbivory and a paucity of dispersers and pollinators. No single dataset or gene identified all taxa in our dataset, demonstrating the value of multiproxy or multigene datasets in studies of animal diets. Our results highlight how contemporary data may considerably underestimate the full dietary breadth of threatened species and demonstrate the potential value of coprolite analysis in conservation biology.

show abstract

Unraveling the dietary diversity of Neotropical top predators using scat DNA metabarcoding: A case study on the elusive Giant Otter

Cited by 12 publications

References 74 publications

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Multiple species‐specific molecular markers using nanofluidic array as a tool to detect prey DNA from carnivore scats

Assessing the Diet of a Predator Using a DNA Metabarcoding Approach

Ancient and modern scats record broken ecological interactions and a decline in dietary breadth of the critically endangered kākāpō parrot (Strigops habroptilus)

Contact Info

Product

Resources

About