Fish gut content analysis: robust measures of diet composition

Abstract

Trophic studies are fundamental components of our understanding of biology and ecology, from observing individual organisms to modelling ecosystem function. When measuring fish gut contents, we rely on collecting samples that represent snapshots in time. Many limitations in extrapolating from these snapshots are well understood. However, there seems to be a widespread belief that when quantifying the composition of gut contents, more detail always provides more information. We highlight some fundamental problems with the apparently more quantitative approaches (i.e. ‘bulk’ methods measuring biomass or volume of each prey type) and suggest that frequency of occurrence (%F) provides the most robust and interpretable measure of diet composition. The additional information provided by bulk methods contains unquantifiable and potentially significant error from a variety of sources. In our experience, the contents of most guts cannot be unambiguously separated into prey categories for quantification because of the presence of unidentifiable and inseparable partially digested material. Even where separation is possible, the composition of a gut at one point in time is affected by many unquantifiable factors unrelated to the actual composition of the diet. Consequently, bulk methods provide ambiguous interpretations from superficially quantitative models. Where research questions require more detail, these problems mean there is little alternative to time‐consuming approaches like prey reconstruction. However, for the descriptions of dietary composition presented in many studies, %F provides robust data that overcome many of the limitations of the more detailed approaches and provides considerable logistical and economic benefits.

Use of DNA metabarcoding for stomach content analysis in the invasive lionfish Pterois volitans in Puerto Rico

“…However, in most cases, partially digested specimens could be identified taxonomically as either fish or invertebrate, but no further. Morphological identification of gut contents relies heavily on the digested state of the prey items (Baker et al 2014). Regardless, this method has been used widely in lionfish feeding ecology.…”

“…The inshore and offshore reefs harbor dissimilar fish richness and biomass (Pittman et al 2010), where inner reefs are comparatively lower in species richness than shelf-edge reefs (Nemeth 2013), thus providing a potential spatial comparison of lionfish diets. Lionfish were collected by pole spear and SCUBA at depths ≤30 m. On the boat, the venomous spines were immediately removed and specimens were placed on ice to slow digestive processes and preserve DNA (Baker et al 2014). All metrics pertaining to lionfish size, sex, reproductive state, and weight were recorded (see Table S1 in the Supplement at www.int-res.com/articles/ suppl/ m558 p181 _supp.pdf).…”

“…using morphological characters to identify whole or only partially digested specimens) or a DNA barcoding approach, which involves sequencing of the mitochondrial 16S rRNA or cytochrome oxidase subunit I (COI) genes from all distinct prey components of the stomach. Morphological identification relies heavily on the ability to identify digested organisms to the species level, which is not possible in many cases (Baker et al 2014). This technique discards useful information that could be obtained in the digested portion of the stomach contents (the liquids or digested pulp).…”

Feeding ecology of the beach silverside Atherinella blackburni (Atherinopsidae) in a tropical sandy beach, Southeastern Brazil

“…A. blackburni diet and importance of each prey item was described by the frequency of occurrence (Fi) and numerical frequency (Ni) of dietary items (BAKER et al, 2014). Fi is the number of individuals containing the item i divided by the total number of analysed individuals.…”

Distribution, feeding and ecomorphology of four species of Auchenipteridae (Teleostei: Siluriformes) in Eastern Amazonia, Brazil

“…Several studies focusing on feeding biology have been conducted in natural communities of freshwater fi sh in Brazil, through a detailed investigation of the feeding habits as an alternative way to analyze the use of habitat by diff erent species (Baker et al, 2014). Indirect methods, as ecomorphology, were also used for the description of the feeding and environmental tactics of the species (Winemiller, 1991;Severo-Neto et al, 2015).…”