A comparison of morphological and molecular diet analyses of predator scats

Abstract

An understanding of a species’ diet is required to make sound conservation and management decisions. Traditionally, morphological analyses of undigested hard parts from food items remaining in scats have been used to assess diets. More recently, molecular analyses of scats have been used to identify plant and prey species’ DNA, but no studies have compared morphological and molecular diet analyses for large, terrestrial carnivores. We used molecular tools to determine the percentage of black bear and coyote scats that contained 3 common prey species (caribou, moose, and snowshoe hares) in Newfoundland and compared the results to a traditional morphological analysis. We found that a ranking of relative prey frequencies was consistent between the 2 methods, but molecular methods tended to detect prey species in a greater percentage of scats for all prey species. However, there were individual scats in which a prey species was detected by morphological methods only, and we provide evidence that molecular methods could result in false negatives if prey DNA is not uniformly distributed throughout a scat or as a result of PCR inconsistency. We also found that the per sample cost comparison between morphological and molecular analyses was dependent upon whether or not a molecular test was needed to identify scats to the predator species, the cost of developing molecular methods, and the number of samples being processed. We recommend that controlled feeding studies be performed to validate molecular methods and investigate the utility of molecular techniques to estimate the proportions of food items consumed.

Promises and pitfalls of using high‐throughput sequencing for diet analysis

“…Faecal analyses come with numerous other challenges. On the one hand are issues related to the sample itself-the eDNA content may not be uniformly distributed throughout a faecal sample (Mumma et al, 2016), which raises the issue of how best to subsample large faecal samples before DNA extraction (Figure 2). On the other hand, DNA from different dietary sources can degrade at differential rates both before and after deposition.…”

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

“…Although metabarcoding applied to dietary studies is now well established, there are still some important limitations to the method, the most important being the lack of a standardized method for quantitative assessment of prey items, as the use of the number of reads belonging to a certain prey as a proxy for its abundance or biomass is not straightforward, nor are the simple counts of sequence reads to estimate the relative levels of prey diversity available (reviewed by Deagle et al, 2019). This is due to many factors, which include biological issues, such as the number of target genes present in each prey cell, body size, and prey digestibility, and also technical factors such as primer annealing bias and PCR random effects (Corse et al, 2019;Darby, Todd, & Herman, 2013;Deagle, Thomas, Shaffer, Trites, & Jarman, 2013;Mumma et al, 2016). The inclusion of mock communities of known composition, sequenced alongside the samples of interest, might allow establishing a direct correlation between the number of reads and the biomass/number of individuals or estimating a correction factor for both biological and technical biases (Thomas et al, 2016), but different outcomes have been obtained from different experiments and the feasibility of such trials varies (reviewed by Deagle et al, 2019).…”

Comparing morphological and molecular diet analyses and fecal DNA sampling protocols for a terrestrial carnivore

“…Genetic analysis of fecal samples provides an alternative method of diet analysis (Symondson , Waits and Paetkau ). Instead of relying on the presence and identification of indigestible prey remains, molecular scatology approaches test for the presence of prey DNA in a predator's scat by using either 1) taxon‐specific primers (Casper et al 2007 a , Egeter et al , Mumma et al ) to test for the presence of DNA from targeted prey groups (e.g., species or genus) or 2) universal primers (Deagle et al , Lopes et al ) to amplify and compare DNA sequences to reference databases to identify prey species with DNA barcoding (Valentini et al , Pompanon et al ). Thus, molecular scatology may identify the presence of prey even when indigestible prey remains not consumed, already excreted or regurgitated, or were degraded too extensively for morphological identification (Casper et al 2007, Deagle et al ).…”

“…Considering the quality of information that molecular scatology provides, few studies have attempted to evaluate and optimize methodological sampling approaches or compare molecular and morphological diet analyses; those that have focused primarily on marine predators (Deagle et al , 2009; Casper et al 2007 a ; Tollit et al ; Egeter et al ; Mumma et al ). Deagle et al () evaluated the frequency of prey detection in the scats of captive Steller sea lions ( Eumetopias jubatus ) fed a prescribed diet under different sampling strategies and found that a homogenized sample provided the highest rate of prey detection.…”

“…Other studies on pinniped diets sampled from distinct fecal lobes (Deagle et al ) or homogenized each scat (Casper et al 2007 a , b ), but these studies did not systematically compare the effectiveness of sampling methods. Mumma et al () assessed the uniformity of prey DNA within 5 coyote ( Canis latrans ) and 5 black bear ( Ursus americanus ) scats by comparing prey species detection at 4 subsamples, but only limited inferences could be made because of the small sample size. All but one comparison between molecular and morphological diet analyses suggested that targeted prey was detected more frequently with molecular than morphological analysis (Casper et al 2007 a , b ; Egeter et al ; Mumma et al ).…”