Conventional and molecular analysis of the diet of gentoo penguins: contributions to assess scats for non-invasive penguin diet monitoring

Abstract

There is a growing search for less invasive methods while studying the diet of Antarctic animals in the wild. Therefore, we compared the diet of gentoo penguins from stomach contents (i.e. through visual identification of prey remains) and scats (i.e. faeces), and further compared prey DNA assay in fresh and old scats. Prey remains identified visually in stomach contents and scats were broadly comparable: the crustaceans and fish were the most important components, with Themisto gaudichaudii clearly being the most frequent and numerous prey species in both sampling methods. By mass, differences in species frequency were observed in stomach contents (Parachaenichthys georgianus) and scats (Champsocephalus gunnari), with the former fish species absent in scats.Differences were detected in the most frequent prey (T. gaudichaudii and Euphausia superba) and in various fish species, most with bigger sizes in scats. Allometric equations to estimate most crustacean's sizes (i.e. relationships between carapace and mass/total length) are needed. For DNA studies, when comparing DNA from fresh and old scats, both provided similar results that, in general, were also similar to the visual analysis. In order to use penguin scats (along with the use of DNA analyses) for monitoring purposes, allometric equations to estimate mass and size of prey (most crustaceans) and better designed species-specific primers are needed for targeting key prey species (e.g.Euphausia superba, T. gaudichaudii). These DNA methodologies can complement other methods (i.e. visual analyses and stomach contents analyses) in monitoring programs of penguins.

Combining stable isotopes, morphological, and molecular analyses to reconstruct the diet of free‐ranging consumers

“…Several studies have reported that using DNA sequencing from fecal or stomach samples increases the diversity of food sources F I G U R E 4 Frequency of occurrence (%FO) of food sources in the diet of black bears during spring and late summer/fall in northern Québec and Labrador (Canada) based on morphological (undigested remains) and molecular analyses (DNA barcoding) of fecal samples. Within a given food source, different letters indicate significant differences (p ≤ .05) between approaches compared to the morphological identification of undigested remains (Egeter et al, 2015;Mumma et al, 2016;Tverin et al, 2019;Xavier et al, 2018). We found that categories and ordinal ranking of food sources detected using morphological and molecular methods converged for both species.…”

“…All animal prey found in the diet of wolves were easily assigned to gender or species based on hair medulla patterns. As estimates for wolves came from stomach contents, both remains and DNA detected are expected to be less degraded than what would have been uncovered in feces given the early steps of the digestive process, and absence of environmental degradation due to exposition to light or other abiotic factors (Alberdi et al, 2019;Xavier et al, 2018). Still, detection of birds' remains in stomachs of wolves was achieved with morphological but not with molecular analyses.…”

“…The complex diet mixture of black bears, a situation typical of omnivores, could also have led to high heterogeneity in prey DNA distribution within a given sample although we used samples taken from different locations on each feces to minimize that potential bias (Alberdi et al, 2019;Gosselin et al, 2017) and included replicates for each sample (Mata et al, 2019). Nevertheless, as pointed out for several species, molecular dietary tracing tools are well suited to highlight the presence of food items undetected by simple visual examination, for example, for items highly degraded through the digestion process (Egeter et al, 2015;Shores et al, 2015;Xavier et al, 2018). In our case, the occurrence of fishes in the diet of bears would have remained undetected without the use of molecular tools.…”

“…Sample quality (usually measured as the DNA degradation rate due to environmental conditions), heterogeneous distribution of DNA in samples, and access to a reliable DNA reference database are additional challenges linked to the use of molecular tools to reconstruct the diet of consumers (Alberdi et al, 2019;Mata et al, 2019;Mumma et al, 2016). Considering the respective limitations of morphological and molecular analyses, studies of species with unknown diet would take advantage of a combined approach, thereby increasing the coverage of potential diet items (Méheust et al, 2014;Xavier et al, 2018). Up to now, many studies comparing the two approaches have been conducted using known diets (controlled conditions) or over a subset of potential food sources for wildlife (Egeter et al, 2015;Granquist, Esparza-Salas, Hauksson, Karlsson, & Angerbjorn, 2018;Mumma et al, 2016;Shores, Mondol, & Wasser, 2015).…”

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

“…In the case of diet studies of aquatic species, this gene has been applied in the same proportion as COI (Figure a). Ultimately, the approach that will warrant best results in terms of taxonomic coverage is the combination of multiple markers (Chen et al, ; McFadden et al, ; Shearer & Coffroth, ), and this has been applied in several dietary studies (Berry et al, ; Pereira et al, ; Xavier et al, ), albeit only about one third of the studies surveyed herein used a multiloci approach (Table S1). Finally, genomic approaches, describing complete organelle genomes and nuclear ribosomal DNA, encompassing many potential barcoding loci, have been suggested as a more accurate and powerful alternative (Coissac et al, ).…”