Development and application of DNA techniques for validating and improving pinniped diet estimates

Marine mammals and microplastics: A systematic review and call for standardisation

Microplastics receive significant societal and scientific attention due to increasing concerns about their impact on the environment and human health. Marine mammals are considered indicators for marine ecosystem health and many species are of conservation concern due to a multitude of anthropogenic stressors. Marine mammals may be vulnerable to microplastic exposure from the environment, via direct ingestion from sea water, and indirect uptake from their prey. Here we present the first systematic review of literature on microplastics and marine mammals, composing of 30 studies in total. The majority of studies examined the gastrointestinal tracts of beached, bycaught or hunted cetaceans and pinnipeds, and found that microplastics were present in all but one study, and the abundance varied between 0 and 88 particles per animal. Additionally, microplastics in pinniped scats (faeces) were detected in eight out of ten studies, with incidences ranging from 0% of animals to 100%. Our review highlights considerable methodological and reporting deficiencies and differences among papers, making comparisons and extrapolation across studies difficult. We suggest best practices to avoid these issues in future studies. In addition to empirical studies that quantified microplastics in animals and scat, ten studies out of 30 (all focussing on cetaceans) tried to estimate the risk of exposure using two main approaches; i) overlaying microplastic in the environment (water or prey) with cetacean habitat or ii) proposing biological or chemical biomarkers of exposure. We discuss advice and best practices on research into the exposure and impact of microplastics in marine mammals. This work on marine ecosystem health indicator species will provide valuable and comparable information in the future.

Large-scale molecular barcoding of prey DNA reveals predictors of intrapopulation feeding diversity in a marine predator

Predator-prey interactions are critical in understanding how communities function. However, we need to describe intraspecific variation in diet to accurately depict those interactions. Harbor seals (Phoca vitulina) are an abundant marine predator that prey on species of conservation concern. We estimated intrapopulation feeding diversity (variation in feeding habits between individuals of the same species) of harbor seals in the Salish Sea. Estimates of feeding diversity were examined relative to sex, month, and location using a novel approach that combined molecular techniques, repeated cross-sectional sampling of scat, and a specialization metric (within-individual consistency in diet measured by the Proportional Similarity Index ( P S i )). Based on 1,083 scat samples collected from five haul-out sites during four nonsequential years, we quantified diet using metabarcoding techniques and determined the sex of the scat depositor using a molecular assay. Results suggest that intrapopulation feeding diversity was present. Specialization was high over short periods (24-48 hr, P S i  = 0.392, 95% CI = 0.013, R = 100,000) and variable in time and space. Females showed more specialization than males, particularly during summer and fall. Additionally, demersal and benthic prey species were correlated with more specialized diets. The latter finding suggests that this type of prey likely requires specific foraging strategies and that there are trade-offs between pelagic and benthic foraging styles for harbor seals. This differential feeding on prey species, as well as between sexes of harbor seals, indicates that predator-prey interactions in harbor seals are complex and that each sex may have a different impact on species of conservation concern. As such, describing intrapopulation feeding diversity may unravel hitherto unknown complex predator-prey interactions in the community.

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

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.

Contemporary diets of walruses in Bristol Bay, Alaska suggest temporal variability in benthic community structure

Background

Pacific walruses (Odobenus rosmarus divergens) are a conspicuous and important component of the Bristol Bay ecosystem and human social systems, but very little is known about walrus ecology in this region, principally their feeding ecology. The present work provides contemporary data on the diets of walruses at four haulout locations throughout Bristol Bay between 2014 and 2018.

Methods

We analyzed scat and gastrointestinal tract samples from these animals using quantitative polymerase chain reaction to amplify prey DNA, which allowed for diet estimates based on frequencies of prey item occurrence and on the relative importance of dietary items as determined from DNA threshold cycle scores.

Results

Diets were highly diverse at all locations, but with some variation in composition that may be related to the time of year that samples were collected (summer vs. autumn), or to spatial variability in the distribution of prey. Overall, polychaetes and tunicates had the highest frequencies of occurrence and relative abundances in 2014-15, but a major change in diet appears to have occurred by 2017-18. While some sample sizes were small, diets in these later years contrasted sharply, with a greater prevalence of sea cucumbers and mollusks, and reduced importance of decapods and fishes compared to the earlier years. Prey identified in scat samples from one collection site also contrasted sharply with those reported from the same location in 1981. The apparent temporal shifts in walrus prey may represent a changing benthic ecosystem due to warming waters in recent decades.

A re-examination of the relationship between Steller sea lion (Eumetopias jubatus) diet and population trend using data from the Aleutian Islands

Prey diversity and energy density have been linked to each other and to population trends in many studies of bird and mammal diets. We re-examined these relationships in Steller sea lions (Eumetopias jubatus (Schreber, 1776)) using data collected from the Aleutian Islands, where there has been a strong longitudinal gradient in population trend. Diet diversity and energy density metrics were similar in the western Aleutians, where sea lion counts declined consistently, and in the easternmost Aleutian area, where population trends improved significantly. We compared traditional deterministic diet diversity metrics with diversity scores based on an occupancy model that accounts for differences in sample size and uncertainty in prey group detection. This analysis indicated that there was no significant change in diet diversity over the 23-year study period or any significant differences across the Aleutian Islands. These results are consistent with prey abundance data from nine groundfish bottom trawl surveys conducted over the same period. While diet studies detail what Steller sea lions eat and provide an estimate of their energy intake, they provide only limited information on the energy expended to obtain their food or the consequences of their diet and foraging ecology on individual or population fitness.

Molecular versus morphological approaches to diet analysis of the caracal (Caracal caracal)

Diet analysis is an essential part in understanding the biology of a species and functioning of ecosystems. Traditional morphological identification of undigested remains in the scats and molecular analyses of prey species’ DNA have previously been used to assess diet. In the present study, caracal diet in the Abbasabad Wildlife Refuge, Central Iran, was investigated using both molecular and morphological methods. We collected 22 scat samples from caracal dens in the region. Feces were washed on sieves and their remaining components were morphologically identified. We also targeted a 307-base pair fragment of the cytochrome b gene to amplify and sequence the species’ DNA. Morphological analyses revealed that 76% of the diet comprised rodent species. We identified a total of nine prey taxa using the molecular method, including six rodents, one hare, one hedgehog and one wild goat. There was a general agreement between the molecular and morphological results; however, molecular methods tended to allow a better identification of the prey species. Therefore, the DNA-based approach acts as a valuable complement to current morphological methods in the study of a rare felid’s diet when no hair reference library exists.

Using molecular diet analysis to inform invasive species management: A case study of introduced rats consuming endemic New Zealand frogs

The decline of amphibians has been of international concern for more than two decades, and the global spread of introduced fauna is a major factor in this decline. Conservation management decisions to implement control of introduced fauna are often based on diet studies. One of the most common metrics to report in diet studies is Frequency of Occurrence (FO), but this can be difficult to interpret, as it does not include a temporal perspective. Here, we examine the potential for FO data derived from molecular diet analysis to inform invasive species management, using invasive ship rats (Rattus rattus) and endemic frogs (Leiopelma spp.) in New Zealand as a case study. Only two endemic frog species persist on the mainland. One of these, Leiopelma archeyi, is Critically Endangered (IUCN 2017) and ranked as the world's most evolutionarily distinct and globally endangered amphibian (EDGE, 2018). Ship rat stomach contents were collected by kill-trapping and subjected to three methods of diet analysis (one morphological and two DNA-based). A new primer pair was developed targeting all anuran species that exhibits good coverage, high taxonomic resolution, and reasonable specificity. Incorporating a temporal parameter allowed us to calculate the minimum number of ingestion events per rat per night, providing a more intuitive metric than the more commonly reported FO. We are not aware of other DNA-based diet studies that have incorporated a temporal parameter into FO data. The usefulness of such a metric will depend on the study system, in particular the feeding ecology of the predator. Ship rats are consuming both species of native frogs present on mainland New Zealand, and this study provides the first detections of remains of these species in mammalian stomach contents.

Absence of Neu5Gc and Presence of Anti-Neu5Gc Antibodies in Humans-An Evolutionary Perspective

The glycocalyx of human cells differs from that of many other mammals by the lack of the sialic acid N-glycolylneuraminic acid (Neu5Gc) and increased abundance of its precursor N-acetylneuraminic acid (Neu5Ac). Most humans also have circulating antibodies specifically targeting the non-human sialic acid Neu5Gc. Recently, several additional mammalian species have been found to also lack Neu5Gc. In all cases, loss-of-function mutations in the gene encoding the sialic acid-modifying enzyme CMAH are responsible for the drastic change in these species. Unlike other glycan antigens, Neu5Gc apparently cannot be produced by microbes, raising the question about the origin of these antibodies in humans. Dietary exposure and presentation on bacteria coating themselves with Neu5Gc from the diet are distinct possibilities. However, the majority of the non-human species that lack Neu5Gc do not consume diets rich in Neu5Gc, making it unlikely that they will have been immunized against this sialic acid. A notable exception are mustelids (ferrets, martens and their relatives) known for preying on various small mammal species rich in Neu5Gc. No studies exist on levels of anti-Neu5Gc antibodies in non-human species. Evolutionary scenarios for the repeated, independent fixation of CMAH loss-of-function mutations at various time points in the past include strong selection by parasites, especially enveloped viruses, stochastic effects of genetic drift, and directional selection via female immunity to paternal Neu5Gc. Convergent evolution of losses of the vertebrate-specific self-glycan Neu5Gc are puzzling and may represent a prominent way in which glycans become agents of evolutionary change in their own right. Such change may include the reconfiguration of innate immune lectins that use self-sialic acids as recognition patterns.

The diet of free-ranging male Steller sea lions (Eumetopias jubatus) in the eastern Bering Sea: a retrospective analysis based on stomach contents of an endangered pinniped

This study illuminates historical diet and foraging locations of endangered western U.S. stock Steller sea lions (Eumetopias jubatus (Schreber, 1776)). Prey were identified from stomachs of 22 males collected in the eastern Bering Sea from the ice edge in March 1985 and nearshore St. Paul Island in September–October 1985 and 1986. Percent frequency of occurrence (PFO) and percent number (PN) were highest for walleye pollock (Gadus chalcogrammus Pallas, 1814; PFO 69%, PN 15%, mean length 17 cm), Pacific herring (Clupea pallasii Valenciennes in Cuvier and Valenciennes, 1847; PFO 62%, PN 16%, mean length 26 cm), shorthorn sculpin (Myoxocephalus scorpius (Linnaeus, 1758); PFO 54%, PN 30%), and Pacific giant octopus (Enteroctopus dofleini (Wülker, 1910); PFO 39%, PN 8%, mean weight 31 kg) in spring, and northern rock sole (Lepidopsetta polyxystra Orr and Matarese, 2000; PFO 78%, PN 47%, mean length 35 cm), Pacific cod (Gadus macrocephalus Tilesius, 1810; PFO 56%, PN 12%, mean length 62 cm), walleye pollock (PFO 44%, PN 7%, mean length 49 cm), and red Irish lord (Hemilepidotus hemilepidotus (Tilesius, 1811); PFO 11%, PN 9%) in fall. Species of Cryptacanthidae, Liparidae, and Zoarcidae were highly represented and exclusive to spring collections. Predictable seasonal concentrations and movements of mature prey along frontal boundaries of the continental shelf and ice edge may be critical to male Steller sea lion fitness during the non-breeding season.

Evaluating the use of stable isotope analysis to infer the feeding ecology of a growing US gray seal (Halichoerus grypus) population

Gray seals (Halichoerus grypus) have been rapidly recolonizing the Northeast US coast, eliciting concern from the fishing industry. However, the ecological effect of this recovery is still unknown and as such, research is needed to better understand how the diet composition of gray seals in US waters will contribute to the ecological impact. While previous research on seal diets has focused on the analysis of hard prey remains, stable isotope analysis presents an alternative method that can be used to describe marine mammal diets when direct observation is impossible. To address this issue, we used stable isotope analysis of gray seal pup vibrissae and lanugo from Monomoy Island, Cape Cod, MA during the 2015/2016 winter breeding season to estimate adult female diet composition during pregnancy. Stable isotope mixing models (SIMM) suggested adult female gray seals were consuming greater amounts of cephalopod prey and less sand lance than previously indicated from analysis of hard prey remains. However, using SIMMs to estimate the diet composition of gray seals remains difficult due to the large number of isotopically similar prey species and uncertainty in tissue-specific, stable isotope trophic enrichment factors. Even so, by combining prey sources into ecologically informative groups and integrating prior information into SIMMs it is possible to obtain additional insights into the diet of this generalist predator.

Improving Marine Ecosystem Models with Biochemical Tracers

Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.

Diet of endangered Steller sea lions (Eumetopias jubatus) in the Aleutian Islands: new insights from DNA detections and bioenergetic reconstructions

The endangered western stock of Steller sea lion (Eumetopias jubatus (Schreber, 1776)) still declines in the western Aleutian Islands and accurate diet information is vital to test leading hypotheses. We undertook the first bioenergetic diet reconstruction using both molecular and hard part prey identifications from >600 scats collected in March–April 2008 and 2012. Atka mackerel (Pleurogrammus monopterygius (Pallas, 1810)) remained a primary prey (17%–27% by energy), but large (mean 60 cm) Pacific cod (Gadus macrocephalus Tilesius, 1810) also emerged as important prey (20%–24%) in a more diverse diet than previously reported, with Cottidae and smooth lumpsucker (Aptocyclus ventricosus (Pallas, 1769)) also contributing ∼10%. DNA detections highlighted a potentially important and previously underestimated prey, giant Pacific octopus (Enteroctopus dofleini (Wülker, 1910) (diet contribution 2%–15%, dependent on prey size assumptions). Although 504 unique DNA identifications resulted in significant increases for cephalopods, Pacific cod, and smooth lumpsucker, hard part alone species rankings were similar to composite ones and bioenergetic species rankings similar to occurrence-based ones. Retention or regurgitation of large cephalopod beaks, the removal of large cod heads, and skeletal fragility of lumpsuckers may explain these differences. DNA identifications provide valuable comparative and complementary prey occurrence data for pinnipeds, but composite diet estimates are optimal.

Forero M, de Stephanis R. Diet of bottlenose dolphins (Tursiops truncatus) from the Gulf of Cadiz: Insights from stomach content and stable isotope analyses

The ecological role of species can vary among populations depending on local and regional differences in diet. This is particularly true for top predators such as the bottlenose dolphin (Tursiops truncatus), which exhibits a highly varied diet throughout its distribution range. Local dietary assessments are therefore critical to fully understand the role of this species within marine ecosystems, as well as its interaction with important ecosystem services such as fisheries. Here, we combined stomach content analyses (SCA) and stable isotope analyses (SIA) to describe bottlenose dolphins diet in the Gulf of Cadiz (North Atlantic Ocean). Prey items identified using SCA included European conger (Conger conger) and European hake (Merluccius merluccius) as the most important ingested prey. However, mass-balance isotopic mixing model (MixSIAR), using δ¹³C and δ¹⁵N, indicated that the assimilated diet consisted mainly on Sparidae species (e.g. seabream, Diplodus annularis and D. bellottii, rubberlip grunt, Plectorhinchus mediterraneus, and common pandora, Pagellus erythrinus) and a mixture of other species including European hake, mackerels (Scomber colias, S. japonicus and S. scombrus), European conger, red bandfish (Cepola macrophthalma) and European pilchard (Sardina pilchardus). These contrasting results highlight differences in the temporal and taxonomic resolution of each approach, but also point to potential differences between ingested (SCA) and assimilated (SIA) diets. Both approaches provide different insights, e.g. determination of consumed fish biomass for the management of fish stocks (SCA) or identification of important assimilated prey species to the consumer (SIA).

Gaining insights into the ecological role of the New Zealand sole (Peltorhamphus novaezeelandiae) through parasites

Despite the fact that tapeworms comprise the bulk of parasite communities of sharks in marine ecosystems, little is known about their life cycles and, more specifically, about the potential intermediate hosts they utilize as transmission routes. In the absence of morphological features required for specific identification of larval tapeworms from potential intermediate hosts, recent molecular advances have contributed to linking larval and adult parasites and, in some instances, uncovering unknown trophic links. Host-parasite checklists are often the first source of information consulted to assess the diversity and host specificity of parasites, and provide insights into parasite identification. However, these host-parasite checklists are only useful if they encompass the full spectrum of associations between hosts and parasites. A checklist of New Zealand fishes and their parasites has been published, but recent parasitological examinations of commercial fish species reveal that the checklist appears to be far from complete. We focused our current study on a comprehensive survey of macroparasites of a commercial species, the New Zealand sole (Peltorhamphus novaezeelandiae) off the coast of Otago, New Zealand. Specifically, we were expecting to recover marine tapeworms using sharks as their definitive hosts that are generally underreported in parasite surveys. The parasites recovered included tapeworms, flukes, round worms and thorny-headed worms. Surprisingly, a large proportion of the non-tapeworm parasites we recovered were not previously reported from this fish species. A discussion on the potential ecological roles played by this fish species in the transmission of parasites is included.

The roles and impacts of human hunter-gatherers in North Pacific marine food webs

There is a nearly 10,000-year history of human presence in the western Gulf of Alaska, but little understanding of how human foragers integrated into and impacted ecosystems through their roles as hunter-gatherers. We present two highly resolved intertidal and nearshore food webs for the Sanak Archipelago in the eastern Aleutian Islands and use them to compare trophic roles of prehistoric humans to other species. We find that the native Aleut people played distinctive roles as super-generalist and highly-omnivorous consumers closely connected to other species. Although the human population was positioned to have strong effects, arrival and presence of Aleut people in the Sanak Archipelago does not appear associated with long-term extinctions. We simulated food web dynamics to explore to what degree introducing a species with trophic roles like those of an Aleut forager, and allowing for variable strong feeding to reflect use of hunting technology, is likely to trigger extinctions. Potential extinctions decreased when an invading omnivorous super-generalist consumer focused strong feeding on decreasing fractions of its possible resources. This study presents the first assessment of the structural roles of humans as consumers within complex ecological networks, and potential impacts of those roles and feeding behavior on associated extinctions.

Maximizing dietary information retrievable from carcasses of Great Cormorants Phalacrocorax carbo using a combined morphological and molecular analytical approach

Avian carcasses can provide important information on the trophic ecology of birds. Usually, the number of carcasses available for examination is limited and therefore it is important to gain as much dietary information per specimen as possible. In piscivorous birds and raptors, the stomach has been the primary source of dietary information, whereas the gut (intestine) has so far been neglected as it usually contains only a few morphologically identifiable hard parts of prey. Molecular approaches have the potential to retrieve dietary information from the gut, although this has not yet been verified. As well as identifying the prey, it is important to estimate any secondary predation to avoid food web errors in dietary analyses. The assignment of accidentally consumed prey is notoriously difficult regardless of the prey identification approach used. In the present study, morphological and molecular analyses were, for the first time, combined to maximize the dietary information retrievable from the complete digestive tract of Great Cormorants Phalacrocorax carbo sinensis. Moreover, a novel approach based on predator-prey size ratios was applied to these piscivorous birds to minimize the number of samples that might contain secondarily predated prey. The stomach contents of the examined birds were found to provide the most dietary information when morphological and molecular analyses were used in combination. However, compared with the morphological approach, the molecular analysis increased the number of fish species detected by 39%. The molecular approach also permitted the identification of fish DNA in the Cormorant guts. Predator-prey size ratios derived from morphological analysis of fish hard parts can reduce the incidence of potential confounding influence of secondarily predated prey by 80%. Our findings demonstrate that a combination of morphological and molecular approaches maximizes the trophic information retrievable from bird carcasses.

A comparison of morphological and molecular diet analyses of predator scats

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.

Stable Isotope Models Predict Foraging Habitat of Northern Fur Seals (Callorhinus ursinus) in Alaska

We developed models to predict foraging habitat of adult female northern fur seals (Callorhinus ursinus) using stable carbon (δ¹³C) and nitrogen (δ¹⁵N) isotope values from plasma and red blood cells. Binomial generalized linear mixed models were developed using blood isotope samples collected from 35 adult female fur seals on three breeding colonies in Alaska during July-October 2006. Satellite location and dive data were used to define habitat use in terms of the proportion of time spent or dives made in different oceanographic/bathymetric domains. For both plasma and red blood cells, the models accurately predicted habitat use for animals that foraged exclusively off or on the continental shelf. The models did not perform as well in predicting habitat use for animals that foraged in both on- and off-shelf habitat; however, sample sizes for these animals were small. Concurrently collected scat, fatty acid, and dive data confirmed that the foraging differences predicted by isotopes were associated with diet differences. Stable isotope samples, dive data, and GPS location data collected from an additional 15 females during August-October 2008 validated the effective use of the models across years. Little within year variation in habitat use was indicated from the comparison between stable isotope values from plasma (representing 1-2 weeks) and red blood cells (representing the prior few months). Constructing predictive models using stable isotopes provides an effective means to assess habitat use at the population level, is inexpensive, and can be applied to other marine predators.

Diet composition of Steller sea lions (Eumetopias jubatus) in Frederick Sound, southeast Alaska: a comparison of quantification methods using scats to describe temporal and spatial variabilities

We compared eight dietary indices used to describe the diet of Steller sea lions (Eumetopias jubatus (Schreber, 1776)) from 2001 to 2004 in Frederick Sound, southeast Alaska. Remains (n = 9666 items) from 59+ species categories were identified from 1684 fecal samples (scats) from 14 collection periods. The most frequently occurring prey were walleye pollock (Theragra chalcogramma (Pallas, 1814) = Gadus chalcogrammus Pallas, 1814; 95%), Pacific herring (Clupea pallasii Valenciennes in Cuvier and Valenciennes, 1847; 30%), Pacific hake (Merluccius productus (Ayres, 1855); 29%), and arrowtooth flounder (Atheresthes stomias (Jordan and Gilbert, 1880) = Reinhardtius stomias (Jordan and Gilbert, 1880); 21%). These species, along with Pacific salmon (genus Oncorhynchus Suckley, 1861) and skate (genus Raja L., 1758), accounted for 80%–90% of the reconstructed biomass and energy contribution, with pollock contributing 37%–60%. Overall, 80% of fish were 14–42 cm long and mainly pelagic, though 40% of scats contained benthic-associated prey. Steller sea lions switched from adult pollock to strong cohorts of juvenile pollock, and took advantage of spawning concentrations of salmon in autumn and herring in late spring and summer, as well as a climate-driven increase in hake availability. Observed temporal and site differences in diet confirm the need for robust long-term scat sampling protocols. All major indices similarly tracked key temporal changes, despite differences in occurrence and biomass-energy-based diet estimates linked to prey size and energy-density effects and the application of correction factors.

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals' diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.

Who is eating what: diet assessment using next generation sequencing

The analysis of food webs and their dynamics facilitates understanding of the mechanistic processes behind community ecology and ecosystem functions. Having accurate techniques for determining dietary ranges and components is critical for this endeavour. While visual analyses and early molecular approaches are highly labour intensive and often lack resolution, recent DNA-based approaches potentially provide more accurate methods for dietary studies. A suite of approaches have been used based on the identification of consumed species by characterization of DNA present in gut or faecal samples. In one approach, a standardized DNA region (DNA barcode) is PCR amplified, amplicons are sequenced and then compared to a reference database for identification. Initially, this involved sequencing clones from PCR products, and studies were limited in scale because of the costs and effort required. The recent development of next generation sequencing (NGS) has made this approach much more powerful, by allowing the direct characterization of dozens of samples with several thousand sequences per PCR product, and has the potential to reveal many consumed species simultaneously (DNA metabarcoding). Continual improvement of NGS technologies, on-going decreases in costs and current massive expansion of reference databases make this approach promising. Here we review the power and pitfalls of NGS diet methods. We present the critical factors to take into account when choosing or designing a suitable barcode. Then, we consider both technical and analytical aspects of NGS diet studies. Finally, we discuss the validation of data accuracy including the viability of producing quantitative data.

PCR enrichment techniques to identify the diet of predators

The increasing sensitivity of PCR has meant that in the last two decades PCR has emerged as a major tool in diet studies, enabling us to refine our understanding of trophic links and to elucidate the diets of predators whose prey is as yet uncharacterized. The achievements and methods of PCR-based diet studies have been reviewed several times, but here we review an important development in the field: the use of PCR enrichment techniques to promote the amplification of prey DNA over that of the predator. We first discuss the success of using group-specific primers either in parallel single reactions or in multiplex reactions. We then concentrate on the more recent use of PCR enrichment techniques such as restriction enzyme digests, peptide nucleic acid clamping, DNA blocking and laser capture microdissection. We also survey the vast literature on enrichment techniques in clinical biology, to ascertain the pitfalls of enrichment techniques and what refinements have yielded some highly sensitive methods. We find that while there are several new approaches to enrichment, peptide nucleic acid clamping and DNA blocking are generally sufficient techniques for the characterization of diets of predators and highlight the most important considerations of the approach.

DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches

The genetic analysis of faecal material represents a relatively non-invasive way to study animal diet and has been widely adopted in ecological research. Due to the heterogeneous nature of faecal material the primary obstacle, common to all genetic approaches, is a means to dissect the constituent DNA sequences. Traditionally, bacterial cloning of PCR amplified products was employed; less common has been the use of species-specific quantitative PCR (qPCR) assays. Currently, with the advent of High-Throughput Sequencing (HTS) technologies and indexed primers it has become possible to conduct genetic audits of faecal material to a much greater depth than previously possible. To date, no studies have systematically compared the estimates obtained by HTS with that of qPCR. What are the relative strengths and weaknesses of each technique and how quantitative are deep-sequencing approaches that employ universal primers? Using the locally threatened Little Penguin (Eudyptula minor) as a model organism, it is shown here that both qPCR and HTS techniques are highly correlated and produce strikingly similar quantitative estimates of fish DNA in faecal material, with no statistical difference. By designing four species-specific fish qPCR assays and comparing the data to the same four fish in the HTS data it was possible to directly compare the strengths and weaknesses of both techniques. To obtain reproducible quantitative data one of the key, and often overlooked, steps common to both approaches is ensuring that efficient DNA isolation methods are employed and that extracts are free of inhibitors. Taken together, the methodology chosen for long-term faecal monitoring programs is largely dependent on the complexity of the prey species present and the level of accuracy that is desired. Importantly, these methods should not be thought of as mutually exclusive, as the use of both HTS and qPCR in tandem will generate datasets with the highest fidelity.

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

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, eulachon 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 faecal DNA can detect the approximate relative quantity of prey consumed for complex diets and prey species, including cephalopods and fish.