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

Abstract

Accurate estimates of animal diet composition are essential to untangle complex interactions in food webs. Biomarkers and molecular tools are increasingly used to estimate diet, sometimes alongside traditional dietary tracing methods. Yet only a few empirical studies have compared the outcomes and potential gains of using a combination of these methods, especially using free‐ranging animals with distinct foraging preferences. We used stable isotopes, morphological, and molecular analyses to investigate the diet of free‐ranging consumers with two distinct diet types, that is, carnivore and omnivore. By combining the three analytical methods to assess the diet of consumers during the same period, we aimed to identify the limits of each method and to assess the potential benefits of their combined use to derive diet estimates. Our results showed that the different methods led to a consistent diet description for carnivores, which have a relatively simple diet mixture, but their outcomes somewhat differed for omnivore, which have a more complex diet. Still, the combined use of morphological and molecular analyses enhanced the diversity of food sources detected compared to the use of a single method independently of diet types. Precision of diet estimates derived from stable isotope analyses was improved by the addition of priors obtained from morphological and molecular diet analyses of the same population. Although we used free‐ranging animals without a known diet, our empirical testing of three of the most widely used methods of diet determination highlights the limits of relying over a single approach, especially in systems with few or no a priori information about the foraging habits of consumers. The choice of an appropriate approach of diet description should be a key step when planning dietary studies of free‐ranging populations. We recommend using more than one dietary determination methods especially for species with complex diet mixtures.

The problem of omnivory: A synthesis on omnivory and DNA metabarcoding

“…Discerning the diet of omnivores is challenging, but DNA metabarcoding has demonstrably facilitated the most comprehensive dietary assessments to date for a number of trophic generalists (Bonin et al, 2020; De Barba et al, 2014; Robeson et al, 2018; Silva et al, 2019), revolutionising the field of trophic ecology. Nevertheless, the problems of secondary predation and accidental consumption are exacerbated when examining the diet of omnivores.…”

“…Dietary metabarcoding has the potential to reveal these omnivores and their trophic interactions, but data will need to be carefully interpreted to accurately elucidate their trophic ecology. More generally, metabarcoding has revolutionised diet assessment and can be used in tandem with other methods (e.g., stable isotope analysis [Hambäck et al, 2016], morphological examination of faeces or gut contents [Brassea‐Pérez et al, 2019] or both [Bonin et al, 2020]) to provide the most comprehensive dietary analyses to date. These methods can therefore help to identify complete ecological networks in a range of environments and with myriad applications.…”

“…More recently, a study on black bears ( Ursus americanus ) in Canada by Bonin et al (2020) used a mixed approach of HTS, morphological examination of faeces, and stable‐isotope analysis to determine diet. Results revealed that black bears consumed a wide variety of vertebrate and plant species.…”

“…The chance of contamination of scats by species found in the immediate environment may also increase with time exposed before sample collection but obtaining samples immediately after excretion is probably challenging in free-ranging populations of black bears. Nevertheless, the use of combined methods by Bonin et al (2020) overcame many of the issues faced by relying solely on one method of dietary determination.…”

DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair’s skink (Leiolopisma telfairii)

“…Identifying the diet of omnivores is challenging, but a few studies have facilitated the most comprehensive complex dietary assessments to date using DNA metabarcoding (Bonin et al, 2020; De Barba et al, 2014; Robeson et al, 2018; Silva et al, 2019). Trophic generalists may be central to ecological networks and can elicit top‐down effects across their entire breadth and depth.…”