Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses

Biffi, M.; Gillet, François; Laffaille, Pascal; Colas, Fanny; Aulagnier, Stéphane; Blanc, F.; Galan, Maxime; Tiouchichine, Marie-Laure; Némoz, Mélanie; Buisson, Laëtitia; Michaux, Johan

doi:10.1093/jmammal/gyx070

Cited by 31 publications

(46 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…From the 194 invertebrate genera identified in the faeces of G. pyrenaicus in the present study, only 61 were common with the 156 genera identified in a previous study using similar genetic methods but conducted in the whole French Pyrenees (Gillet, 2015;Biffi et al, 2017). Newly identified prey included an amphibian, aquatic and terrestrial snails, leeches, earwigs, Hydracarina, Chilopoda, Maxillopoda and Collembola.…”

Section: Novel Insights Into the Diet Of G Pyrenaicus And N Fodiensmentioning

confidence: 53%

“…Their main advantages are that (i) they do not request animal sacrifice compared to gut content analysis, (ii) they identify prey with high taxonomic resolution (genus and species levels), (iii) including highly degraded or soft-bodied species (molluscs, earthworms) that cannot be identified morphologically, (iv) they are less time consuming, and (v) they do not require any taxonomical expertise of the range of potential prey as long as taxa are present in genetic databases (see Pompanon et al, 2012 for a review). To date, though the diet of G. pyrenaicus has been recently described using molecular methods (Gillet, 2015;Gillet et al, 2015;Biffi et al, 2017), such data about N. fodiens have never been gathered, making any comparison of the respective diets of these two species rather speculative.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

et al. 2017

Self Cite

View full text Add to dashboard Cite

a b s t r a c tIn this study, the interactions between two semi-aquatic mammals, the endangered Pyrenean desman Galemys pyrenaicus and the Eurasian water shrew Neomys fodiens, were investigated through the analysis of their summer diet using next-generation sequencing methods, combined with analyses of prey selectivity and trophic overlap. The diet of these predators was highly diverse including 194 and 205 genera for G. pyrenaicus and N. fodiens respectively. Overall, both species exhibited rather non-selective foraging strategies as the most frequently consumed invertebrates were also the most frequent and abundant in the streams. This supported a generalist foraging behaviour for G. pyrenaicus and N. fodiens in the study area. The Pianka index (0.4) indicated a significant but moderate dietary overlap as G. pyrenaicus mostly relied on prey with aquatic stages whereas prey of N. fodiens were mainly terrestrial. Moreover, no difference in G. pyrenaicus prey consumption was found in presence or absence of N. fodiens. A differential use of trophic resources through mechanisms such as plastic feeding behaviour or differences in foraging micro-habitat are likely to facilitate the coexistence between these two mammal species.

show abstract

Section: Novel Insights Into the Diet Of G Pyrenaicus And N Fodiensmentioning

confidence: 53%

Section: Introductionmentioning

confidence: 99%

Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

et al. 2017

Self Cite

View full text Add to dashboard Cite

show abstract

“…(). Its efficiency to identify a wide taxonomic range of arthropods from France has been proven recently: 20 arthropod orders were detected in the diet of Galemys pyrenaicus and 24 in the diet of Neomys fodiens (Biffi, Gillet, et al., ; Biffi, Laffaille, et al., ). We have verified the discriminatory power of this minibarcode for resolving bat species identification using an in silico analysis based on 444 bold (Barcode of Life DataBase) reference sequences corresponding to the 33 bat species found in France (see the phylogenetic tree provided in Figure S1 and the Table S2).…”

Section: Methodsmentioning

confidence: 99%

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

Galan

Pons

Tournayre

et al. 2018

Molecular Ecology Resources

Self Cite

159

157

View full text Add to dashboard Cite

Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.

show abstract

“…Another issue is the impact of collecting data with markers that have low taxonomic resolution (McInnes, Alderman, Lea, et al., ) or collating data at higher taxonomic levels to increase certainty in taxonomic assignment (Biffi et al., ). Depending on how broad the groupings are, occurrence summaries may not be very informative as many occurrences are potentially pooled.…”

Section: A View Of the Way Forward In Interpreting Sequence Countsmentioning

confidence: 99%

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

et al. 2018

View full text Add to dashboard Cite

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

show abstract

Novel insights into the diet of the Pyrenean desman (Galemys pyrenaicus) using next-generation sequencing molecular analyses

Cited by 31 publications

References 45 publications

Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

Comparison of diet and prey selectivity of the Pyrenean desman and the Eurasian water shrew using next-generation sequencing methods

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Contact Info

Product

Resources

About