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

Testing for effects of growth rate on isotope trophic discrimination factors and evaluating the performance of Bayesian stable isotope mixing models experimentally: A moment of truth?

Discerning assimilated diets of wild animals using stable isotopes is well established where potential dietary items in food webs are isotopically distinct. With the advent of mixing models, and Bayesian extensions of such models (Bayesian Stable Isotope Mixing Models, BSIMMs), statistical techniques available for these efforts have been rapidly increasing. The accuracy with which BSIMMs quantify diet, however, depends on several factors including uncertainty in tissue discrimination factors (TDFs; Δ) and identification of appropriate error structures. Whereas performance of BSIMMs has mostly been evaluated with simulations, here we test the efficacy of BSIMMs by raising domestic broiler chicks (Gallus gallus domesticus) on four isotopically distinct diets under controlled environmental conditions, ideal for evaluating factors that affect TDFs and testing how BSIMMs allocate individual birds to diets that vary in isotopic similarity. For both liver and feather tissues, δ13C and δ 15N values differed among dietary groups. Δ13C of liver, but not feather, was negatively related to the rate at which individuals gained body mass. For Δ15N, we identified effects of dietary group, sex, and tissue type, as well as an interaction between sex and tissue type, with females having higher liver Δ15N relative to males. For both tissues, BSIMMs allocated most chicks to correct dietary groups, especially for models using combined TDFs rather than diet-specific TDFs, and those applying a multiplicative error structure. These findings provide new information on how biological processes affect TDFs and confirm that adequately accounting for variability in consumer isotopes is necessary to optimize performance of BSIMMs. Moreover, results demonstrate experimentally that these models reliably characterize consumed diets when appropriately parameterized.

Use of stable isotopes to reveal trophic relationships and transmission of a food-borne pathogen

Predators in food webs are valuable sentinel species for zoonotic and multi-host pathogens such as Toxoplasma gondii. This protozoan parasite is ubiquitous in warm-blooded vertebrates, and can have serious adverse effects in immunocompromised hosts and foetuses. In northern ecosystems, T. gondii is disproportionately prevalent in Inuit people and wildlife, in part due to multiple routes of transmission. We combined data on T. gondii infection in foxes from Nunavik (northern Québec, Canada) with stable isotope data tracking trophic relationships between foxes and several of their main prey species. Red (Vulpes vulpes) and Arctic fox (Vulpes lagopus) carcasses were collected by local trappers from 2015 to 2019. We used magnetic capture PCR to detect DNA of T. gondii in heart and brain tissues, and enzyme-linked immunosorbent assay to detect antibodies in blood. By linking infection status with diet composition, we showed that infected foxes had a higher probability of consuming aquatic prey and migratory geese, suggesting that these may be important sources of T. gondii transmission in the Arctic. This use of stable isotopes to reveal parasite transmission pathways can be applied more broadly to other foodborne pathogens, and provides evidence to assess and mitigate potential human and animal health risks associated with T. gondii in northern ecosystems.

An invasive appetite: Combining molecular and stable isotope analyses to reveal the diet of introduced house mice (Mus musculus) on a small, subtropical island

House mice (Mus musculus) pose a conservation threat on islands, where they adversely affect native species' distributions, densities, and persistence. On Sand Island of Kuaihelani, mice recently began to depredate nesting adult mōlī (Laysan Albatross, Phoebastria immutabilis). Efforts are underway to eradicate mice from Sand Island, but knowledge of mouse diet is needed to predict ecosystem response and recovery following mouse removal. We used next-generation sequencing to identify what mice eat on Sand Island, followed by stable isotope analysis to estimate the proportions contributed by taxa to mouse diet. We collected paired fecal and hair samples from 318 mice between April 2018 to May 2019; mice were trapped approximately every eight weeks among four distinct habitat types to provide insight into temporal and spatial variation. Sand Island's mice mainly consume arthropods, with nearly equal (but substantially smaller) contributions of C3 plants, C4 plants, and mōlī. Although seabird tissue is a small portion of mouse diet, mice consume many detrital-feeding arthropods in and around seabird carcasses, such as isopods, flesh flies, ants, and cockroaches. Additionally, most arthropods and plants eaten by mice are non-native. Mouse diet composition differs among habitat types but changes minimally throughout the year, indicating that mice are not necessarily limited by food source availability or accessibility. Eradication of house mice may benefit seabirds on Sand Island (by removing a terrestrial, non-native predator), but it is unclear how arthropod and plant communities may respond and change. Non-native and invasive arthropods and plants previously consumed (and possibly suppressed) by mice may be released post-eradication, which could prevent recovery of native taxa. Comprehensive knowledge of target species' diet is a critical component of eradication planning. Dietary information should be used both to identify and to monitor which taxa may respond most strongly to invasive species removal and to assess if proactive, pre-eradication management activities are warranted.

DNA metabarcoding the diet of Podarcis lizards endemic to the Balearic Islands

Dietary studies are essential to unravel the functioning of ecosystems and ultimately to understand biodiversity. This task, which at first may seem simple, becomes especially complex in those cases of omnivorous species with highly variable diets. In this regard, the emergence of next-generation DNA sequencing methodologies represents a powerful tool to address the problem. Here we implement a high-throughput metabarcoding strategy based on the analysis of four molecular markers aimed at sequencing both mitochondrial (animal prey) and chloroplast (diet plants) genome fragments from fecal samples of two lizard species endemic to the Balearic Archipelago (Podarcis lilfordi and P. pityusensis) obtained through non-invasive methods. The results allowed for the characterization of their diets with a high degree of taxonomic detail and have contributed a large number of new trophic records. The reported diets are based mainly on the consumption of arthropods, mollusks and plants from a diversity of taxonomic orders, as well as carrion and marine subsidies. Our analyses also reveal inter- and intra-specific differences both in terms of seasonality and geographical distribution of the sampled lizard populations. These molecular findings provide new insights into the trophic interactions of these threatened endemic lizards in their unique and isolated ecosystems.

Diet flexibility of wolves and black bears in the range of migratory caribou

The diet of predators can be highly variable, which is exemplified by their ability to acclimate to a wide range of ecological conditions. Such flexibility in foraging may be a key aspect of their performance in unpredictable environments such as at the edge of the range of a species or where food availability varies greatly in time and space. Gaining information on the diets of predators under such conditions could foster our comprehension of their ecological flexibility and the potential role of predation on the population dynamics of prey. We determined the diet of wolves (Canis lupus) and black bears (Ursus americanus) in northern Québec and Labrador (Canada) within the range of two migratory caribou (Rangifer tarandus) herds: the high-abundance Rivière-aux-Feuilles herd (RFH) and low-abundance Rivière-George herd (RGH). Worldwide, decline in caribou populations has become a concern, stressing the need to better understand the factors involved in these declines, including predation. In northern Québec (RFH range), caribou was the primary year-round prey of wolves while moose (Alces alces) and muskoxen (Ovibos moschatus) were consumed in some sectors. The diet of wolves in northern Labrador (RGH range) varied seasonally, with caribou, moose, and fish as main prey during different periods throughout the year. Black bear diets varied seasonally and regionally. Among the foods we analyzed, caribou was the main source of animal protein for bears in northern Québec and northern Labrador, except during a high abundance of Ungava collared lemming (Dicrostonyx hudsonius). Only bears in northern Québec ate caribou during late summer/fall. Our results highlight the diet flexibility of wolves and black bears in northern food webs, and how their diets change in relation to the distribution and abundance of prey. Our results will help quantify the potential impact of these predators on prey populations in northern systems.

Using eDNA metabarcoding to understand the effect of fire on the diet of small mammals in a woodland ecosystem

Food acquisition is a fundamental process that drives animal distribution and abundance, influencing how species respond to changing environments. Disturbances such as fire create significant shifts in available dietary resources, yet, for many species, we lack basic information about what they eat, let alone how they respond to a changing resource base. In order to create effective management strategies, faunal conservation in flammable landscapes requires a greater understanding of what animals eat and how this change following a fire. What animals eat in postfire environments has received little attention due to the time‐consuming methodologies and low‐resolution identification of food taxa. Recently, molecular techniques have been developed to identify food DNA in scats, making it possible to identify animal diets with enhanced resolution. The primary aim of this study was to utilize eDNA metabarcoding to obtain an improved understanding of the diet of three native Australian small mammal species: yellow‐footed antechinus (Antechinus flavipes), heath mouse (Pseudomys shortridgei), and bush rat (Rattus fuscipes). Specifically, we sought to understand the difference in the overall diet of the three species and how diet changed over time after fire. Yellow‐footed antechinus diets mostly consisted of moths, and plants belonging to myrtles and legume families while bush rats consumed legumes, myrtles, rushes, and beetles. Heath mouse diet was dominated by rushes. All three species shifted their diets over time after fire, with most pronounced shifts in the bush rats and least for heath mice. Identifying critical food resources for native animals will allow conservation managers to consider the effect of fire management actions on these resources and help conserve the species that use them.

DNA metabarcoding reveals that coyotes in New York City consume wide variety of native prey species and human food

Carnivores are currently colonizing cities where they were previously absent. These urban environments are novel ecosystems characterized by habitat degradation and fragmentation, availability of human food, and different prey assemblages than surrounding areas. Coyotes (Canis latrans) established a breeding population in New York City (NYC) over the last few decades, but their ecology within NYC is poorly understood. In this study, we used non-invasive scat sampling and DNA metabarcoding to profile vertebrate, invertebrate, and plant dietary items with the goal to compare the diets of urban coyotes to those inhabiting non-urban areas. We found that both urban and non-urban coyotes consumed a variety of plants and animals as well as human food. Raccoons (Procyon lotor) were an important food item for coyotes within and outside NYC. In contrast, white-tailed deer (Odocoileus virginianus) were mainly eaten by coyotes inhabiting non-urban areas. Domestic chicken (Gallus gallus) was the human food item found in most scats from both urban and non-urban coyotes. Domestic cats (Felis catus) were consumed by urban coyotes but were detected in only a small proportion of the scats (<5%), which differs markedly from high rates of cat depredation in some other cities. In addition, we compared our genetic metabarcoding analysis to a morphological analysis of the same scat samples. We found that the detection similarity between the two methods was low and it varied depending on the type of diet item.

DNA metabarcoding across disciplines: sequencing our way to greater understanding across scales of biological organization

DNA metabarcoding describes the use of targeted DNA (i.e., amplicon) sequencing to identify community constituents from a complex sample containing genetic material from multiple organisms, such as water, soil, gut contents, microbiomes, or biofilms. This molecular approach for characterizing mixed DNA samples relies on the development of "universal primers" that allow for effective amplification of target sequences across a broad range of taxa. Armed with optimized lab protocols and rigorous bioinformatics tools, DNA metabarcoding can produce a wealth of information about the hidden biodiversity of various sample types by probing for organisms' molecular footprints. DNA metabarcoding has received considerable popular press over the last few years because of gut microbiome studies in humans and beyond. However, there are many other applications that are continually integrating molecular biology with other fields of study to address questions that have previously been unanswerable, for both prokaryotic and eukaryotic targets. For example, we can now sample mostly-digested gut contents from virtually any organism to learn about ontogeny and foraging ecology. Water samples collected from different locations can be filtered to extract eDNA (i.e., environmental DNA), revealing the biodiversity of fishes and other taxa targeted by carefully selected primer sets. This universal primer metabarcoding approach has even been extended to looking at diverse gene families within single species, which is particularly useful for complex immune system genetics. The purpose of this SICB symposium was to bring together researchers using DNA metabarcoding approaches to (a) showcase the diversity of applications of this technique for addressing questions spanning ecology, evolution, and physiology, and (b) to spark connections among investigators from different fields that are utilizing similar approaches to facilitate optimization and standardization of metabarcoding methods and analyses. The resulting manuscripts from this symposium represent a great diversity of metabarcoding applications and taxonomic groups of interest.

Sea Snacks from DNA Tracks: Using DNA Metabarcoding to Characterize The Diet of Green Turtles (Chelonia Mydas)

The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.

Integrating DNA-based Prey Occurrence Probability Into Stable Isotope Mixing Models

The introduction of laboratory methods to animal dietary studies has allowed researchers to obtain results with accuracy and precision not possible with observational techniques. For example, DNA barcoding, or the identification of prey with taxon-specific DNA sequences, allows researchers to classify digested prey tissues to the species-level, while stable isotope analysis paired with Bayesian mixing models can quantify dietary contributions by comparing a consumer's isotopic values to those derived from their prey. However, DNA-based methods are currently only able to classify, but not quantify, the taxa present in a diet sample, while stable isotope analysis can only quantify dietary taxa that are identified a priori as prey isotopic values are a result of life history traits, not phylogenetic relatedness. Recently, researchers have begun to couple these techniques in dietary studies to capitalize on the reciprocal benefits and drawbacks offered by each approach, with some even integrating DNA-based results directly into Bayesian mixing models as informative priors. As the informative priors used in these models must represent known dietary compositions (e.g., percentages of prey biomasses), researchers have scaled the DNA-based frequency of occurrence of major prey groups so that their normalized frequency of occurrence sums to 100%. Unfortunately, such an approach is problematic as priors stemming from binomial, DNA-based data do not truly reflect quantitative information about the consumer's diet and may skew the posterior distribution of prey quantities as a result. Therefore, we present a novel approach to incorporate DNA-based dietary information into Bayesian stable isotope mixing models that preserves the binomial nature of DNA-based results. This approach uses community-wide frequency of occurrence or logistic regression-based estimates of prey occurrence to dictate the probability that each prey group is included in each mixing model iteration, and, in turn, the probability that each iteration's results are included in the posterior distribution of prey composition possibilities. Here, we demonstrate the utility of this method by using it to quantify the prey composition of nestling Louisiana waterthrush (Parkesia motacilla).

Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie

Diet analysis integrates a wide variety of visual, chemical, and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, for example, highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package mvtweedie that extends capabilities of widely used packages in R (mgcv and ggplot2) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted Puffins (Fratercula cirrhata) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980–2000) and then Pacific herring and capelin (2000–2020), while wolves (Canis lupus ligoni) in southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines.

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

Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.

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

Dietary analysis using DNA metabarcoding is a powerful tool that is increasingly being used to further our knowledge of trophic interactions in highly complex food webs but is not without limitations. Omnivores, the most generalist of consumers, pose unique challenges when using such methods. Here, we provide the rationale to understand the problems associated with analysing the complex diets of omnivores. By reviewing existing metabarcoding studies of omnivorous diet, and constructing hypothetical scenarios arising from each, we outline that great caution is required when interpreting sequencing data in such cases. In essence, the problems of accidental consumption and secondary ingestion are significant sources of error when investigating omnivorous diets. The integration of multiple high throughput sequencing markers increases the taxonomic breadth of taxa detected but we reveal how some detections may be misleading. Disentangling which taxa have been deliberately or accidentally consumed by the focal omnivore is challenging and can falsely emphasise those that were not intentionally consumed, obscuring biologically meaningful interactions. Although we suggest ways to disentangle these issues, we urge that the results of such analyses should be interpreted with caution and all possible scenarios for the presence of biota within omnivores given due consideration.