Determining diet is a key prerequisite for understanding species interactions, food web structure and ecological dynamics. In recent years, there has been considerable development in both the methodology and application of novel and more traditional dietary tracing methods, yet there is no comprehensive synthesis that systematically and quantitatively compares the different approaches.
Here we conceptualise diet tracing in ecology, provide recommendations for method selection, and illustrate the advantages of method integration. We summarise empirical evidence on how different methods quantify diet mixtures, by contrasting estimates of dietary proportions from multiple methods applied to the same consumer-resource datasets, or from experimental studies with known diet compositions.
Our data synthesis revealed an urgent need for more experiential comparisons among the dietary methods. The comparison of diet quantifications from field observations showed that different techniques aligned well in cases with less than six diet items, but diverged considerably when applied to more complex diet mixtures.
Efforts are ongoing to further advance dietary estimation, including how reliably compound specific stable isotope analyses and fatty acid profiles can quantify more prey items than bulk stable isotope analyses. Similarly, DNA analyses, which can depict trophic interactions at a higher resolution than any other method, are generating new ways to better quantify diets and differentiate among life-stages of prey. Such efforts, combined with more empirical testing of each dietary method and establishment of open data repositories for dietary data, promise to greatly advance community and ecosystem ecology.

https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12869

Diet tracing in ecology: Method comparison and selection

Food web structure, predator–prey dynamics, foraging behavior, and consequences of these factors for individual growth, reproduction and survival are central to our understanding of ecosystem structure and functioning. Moreover, in the current context of understanding (and managing) ecosystems in the face of ongoing environmental change, important questions include: What are the critical prey of key consumers in relation to prey abundance, availability, and nutritional quality? What are the ecosystem processes responsible for food web production? And, how do these processes respond to changes in physical forcing? A fundamental require-ment to understand any of these areas is an accurate assessment of trophic relationships and consumer diets. However, in aquatic, and especially marine ecosystems, such information is generally not easily or reliably obtained. In these systems, the relative inaccessibility of free-ranging organisms and the inability to directly observe species interactions make it difficult to accurately characterize diet. Traditional approaches, such as examining gut contents, have well-recognized biases in addition to representing only snapshots of recent meals and may therefore not be reliable indicators of long-term diet (Iverson et al. 2004). Thus, alternative approaches have been developed, which use various types of trophic markers. One of the most promising of these approaches is the use of lipids and fatty acids (FA) to study food web dynamics.

/pdf/tracing-aquatic-food-webs-using-fatty-acids-from-qualitative-4ku95x47jx.pdf

Tracing aquatic food webs using fatty acids: from qualitative indicators to quantitative determination

Diet estimation in marine mammals relies on indirect methods including recovery of prey hard parts from stomachs and feces, quantitative fatty acid signature analysis (QFASA), stable isotope mixing models, and identification of prey DNA in stomach contents and feces Experimental evidence (9 species/13 studies) shows that digestion strongly influences the proportion and size of otoliths that can be recovered in feces Number correction factors (NCF) and digestion coefficients have been experimentally determined to reduce the biases in fecal analysis Correction factors and coefficients have not been determined for diet estimated from stomach contents QFASA estimates which prey species and amounts must have been eaten to account for the fatty acid composition of the predator Experimental studies on mammals and seabirds (9 species/10 studies) indicate that accurate estimates of diet can be determined using QFASA Stable isotope mixing models provide rather coarse taxonomic resolution of diet composition Prey DNA analysis shows promise as a method to estimate the species composition of diet, but further development and testing is needed to validate its use Obtaining a representative sample from marine mammal populations is a significant challenge Therefore, the use of complementary methods is recommended to obtain the most informative results

/pdf/methods-of-estimating-marine-mammal-diets-a-review-of-n4rassnv8k.pdf

Methods of estimating marine mammal diets: A review of validation experiments and sources of bias and uncertainty

During 2017, the Vancouver Fraser Port Authority's Enhancing Cetacean Habitat and Observation program carried out a two-month voluntary vessel slowdown trial to determine whether slowing to 11 knots was an effective method for reducing underwater radiated vessel noise. The trial was carried out in Haro Strait, British Columbia, in critical habitat of endangered southern resident killer whales. During the trial, vessel noise measurements were collected next to shipping lanes on two hydrophones inside the Haro Strait slowdown zone, while a third hydrophone in Strait of Georgia measured vessels noise outside the slowdown zone. Vessel movements were tracked using the automated identification system (AIS), and vessel pilots logged slowdown participation information for each transit. An automated data processing system analyzed acoustical and AIS data from the three hydrophone stations to calculate radiated noise levels and monopole source levels (SLs) of passing vessels. Comparing measurements of vessels participating in the trial with measurements from control periods before and after the trial showed that slowing down was an effective method for reducing mean broadband SLs for five categories of piloted commercial vessels: containerships (11.5 dB), cruise vessels (10.5 dB), vehicle carriers (9.3 dB), tankers (6.1 dB), and bulkers (5.9 dB).

Slowing deep-sea commercial vessels reduces underwater radiated noise.

Reconstructing the diets of pinnipeds by visually identifying prey remains recovered in faecal samples is challenging 
because of differences in digestion and passage rates of hard parts. Analysing the soft-matrix of faecal material using 
DNA-based techniques is an alternative means to identify prey species consumed, but published techniques are largely 
nonquantitative, which limits their usefulness for some applications. We further developed and validated a real-time PCR 
technique using species-speciﬁc mitochondrial DNA primers to quantify the proportion of prey in the diets of Steller sea 
lions (Eumetopias jubatus), a pinniped species thought to be facing signiﬁcant diet related challenges in the North Paciﬁc. 
We ﬁrst demonstrated that the proportions of prey tissue DNA in mixtures of DNA isolated from four prey species could 
be estimated within a margin of 
􏰁12% of the percent in the mix. These prey species included herring Clupea palasii, eula- 
chon Thaleichthyes paciﬁcus, squid Loligo opalescens and rosethorn rockﬁsh Sebastes helvomaculatus. We then applied 
real-time PCR to DNA extracted from faecal samples obtained from Steller sea lions in captivity that were fed 11 different 
combinations of herring, eulachon, squid and Paciﬁc ocean perch rockﬁsh (Sebastes alutus), ranging from 7% to 75% 
contributions per meal (by wet weight). The difference between the average percentage estimated by real-time PCR and 
the percentage of prey consumed was generally < 12% for all diets fed. Our ﬁndings indicate that real-time PCR of fae- 
cal DNA can detect the approximate relative quantity of prey consumed for complex diets and prey species, including 
cephalopods and ﬁsh.

Proportion of prey consumed can be determined from faecal DNA using real-time PCR.

Reliable estimates of diets are vital to monitor impacts of sea lion populations on their ecosystems and their interactions with fisheries, and to understand the role of food to animal nutrition and health. Approaches include using (1) prey remnants in stomach contents, spews and scats; (2) prey DNA in scats; (3) fatty acid signatures in blubber; and (4) stable isotope ratios in predator’s tissue. Each methodology has particular advantages and limitations, many of which can be assessed and improved through controlled captive feeding trials. Analysis of prey remnants from captive sea lion scats have shown significant variability in digestion between and within prey species, which, coupled with preferential regurgitation and enumeration biases, can confound accurate diet quantification, but does not prevent spatial or temporal comparisons. Correction for partial digestion and use of additional structures besides otoliths can provide reliable prey size estimates. Prey DNA can be consistently isolated from soft remains in scats from captive sea lions, and with further development this approach may allow quantification of diet. Genetic methods can be expensive and representative of only one to two Sea Lions of the World 293 Alaska Sea Grant College Program • AK-SG-06-01, 2006 Tollit et al.—Estimating Diet Composition in Sea Lions days foraging (like prey remnant analysis), but may be less affected by differential digestion and can identify prey in scats that could not be identified through structural remnants. Validation of fatty acid signature analysis to quantify diet at longer temporal scales in sea lions is ongoing. This new technique promises to be particularly useful to assess biases in traditional methods, identify the onset of weaning, and highlight the prey that most contribute to lipid reserves. Stable isotope analysis of predator tissues gives only trophic level data, but can provide data on diet changes on many temporal scales. Remote video monitoring of foraging events and lavage/enema techniques can provide valuable diet information, but, like many newer techniques, animal capture is required. Ideally a suite of techniques should be used to study diet. While methods and correction factors developed for Steller sea lions can likely be applied to the other five sea lion species, they should be verified experimentally. Introduction Reliable estimates of diets are vital to monitor impacts of sea lion populations on their ecosystems and their interactions with fisheries, and to understand the role of food to animal nutrition and health. The traditional approach was to examine stomach contents. More recent methods include using hard remains in scats and spews, isolating prey DNA from scats, fatty acid signatures in blubber, stable isotope ratios in predators’ tissues, and direct video observation. All methods of estimating diet have pros and cons (Table 1), many of which can be assessed and improved through controlled captive feeding trials. Methods Captive feeding studies with 2-5 year old female Steller sea lions at the Vancouver Aquarium Marine Science Centre have assessed three different methods to quantify diet. In this review, we summarize the findings of these studies, complement them with results from additional captive studies with sea lions, and discuss the benefits and drawbacks of alternate techniques presently being used to study sea lion diet (Table 1). 1. Prey remains found in scats The analysis of prey skeletal structures found in scats (feces) is now the most widely used technique for estimating the diet of pinnipeds, with sagittal otoliths being the most commonly used identifying structure (Frost and Lowry 1980, Olesiuk et al. 1990, Bowen et al. 1993, Tollit and Thompson 1996). However, there remain a number of well recognized problems related to identifying prey without hard remains, differential rates of digestion (hence, recovery), and choice of skeletal structures used to identify prey (see reviews by Pierce and Boyle 1991, Bowen 2000). 294 Sea Lions of the World T a b le 1 . P ro s a n d c o n s o f d iff e re n t m e th o d s u s e d t o e s ti m a te d ie t in o ta ri id s .

Estimating diet composition in sea lions: Which technique to choose?

Empirical measures of harbor seal behavior and avoidance of an operational tidal turbine.

Proposed metrics for the management of underwater noise for southern resident killer whales

/pdf/study-of-the-acoustic-effects-of-hydrokinetic-tidal-turbines-23j3vmuhrw.pdf

Study of the Acoustic Effects of Hydrokinetic Tidal Turbines in Admiralty Inlet, Puget Sound

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Estimating diet composition in sea lions: Which technique to choose?

Empirical measures of harbor seal behavior and avoidance of an operational tidal turbine.

Proposed metrics for the management of underwater noise for southern resident killer whales

Study of the Acoustic Effects of Hydrokinetic Tidal Turbines in Admiralty Inlet, Puget Sound